[med-svn] [ariba] branch pristine-tar updated (e58db44 -> 2605220)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch pristine-tar in repository ariba. from e58db44 pristine-tar data for ariba_2.10.1+ds.orig.tar.xz new 2605220 pristine-tar data for ariba_2.10.3+ds.orig.tar.xz The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: ariba_2.10.3+ds.orig.tar.xz.delta | Bin 0 -> 20101 bytes ariba_2.10.3+ds.orig.tar.xz.id| 1 + 2 files changed, 1 insertion(+) create mode 100644 ariba_2.10.3+ds.orig.tar.xz.delta create mode 100644 ariba_2.10.3+ds.orig.tar.xz.id -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] 03/03: new upstream release
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository ariba. commit 219815654fa9f6754d4120a7531eb4b984a67061 Author: Sascha Steinbiss Date: Wed Nov 29 10:42:16 2017 +0100 new upstream release --- debian/changelog | 6 ++ 1 file changed, 6 insertions(+) diff --git a/debian/changelog b/debian/changelog index 308cdae..e138986 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +ariba (2.10.3+ds-1) unstable; urgency=medium + + * New upstream release. + + -- Sascha Steinbiss Tue, 28 Nov 2017 17:01:36 +0100 + ariba (2.10.1+ds-1) unstable; urgency=medium * New upstream release. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] branch upstream updated (1b8ded5 -> e3b0c67)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch upstream in repository ariba. from 1b8ded5 New upstream version 2.10.1+ds new e3b0c67 New upstream version 2.10.3+ds The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: ariba/mlst_reporter.py | 2 +- ariba/ref_genes_getter.py | 4 ++-- ariba/report_filter.py | 2 +- ariba/tests/data/mlst_reporter.het_snps.out.details.tsv | 2 +- setup.py| 2 +- 5 files changed, 6 insertions(+), 6 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] branch master updated (d7e7036 -> 2198156)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch master in repository ariba. from d7e7036 new upstream release new e3b0c67 New upstream version 2.10.3+ds new a51ef9f Update upstream source from tag 'upstream/2.10.3+ds' new 2198156 new upstream release The 3 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: ariba/mlst_reporter.py | 2 +- ariba/ref_genes_getter.py | 4 ++-- ariba/report_filter.py | 2 +- ariba/tests/data/mlst_reporter.het_snps.out.details.tsv | 2 +- debian/changelog| 6 ++ setup.py| 2 +- 6 files changed, 12 insertions(+), 6 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] 01/01: pristine-tar data for ariba_2.10.3+ds.orig.tar.xz
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch pristine-tar in repository ariba. commit 260522080f07c2fdf42f623d9569117d29237eb0 Author: Sascha Steinbiss Date: Tue Nov 28 16:59:32 2017 +0100 pristine-tar data for ariba_2.10.3+ds.orig.tar.xz --- ariba_2.10.3+ds.orig.tar.xz.delta | Bin 0 -> 20101 bytes ariba_2.10.3+ds.orig.tar.xz.id| 1 + 2 files changed, 1 insertion(+) diff --git a/ariba_2.10.3+ds.orig.tar.xz.delta b/ariba_2.10.3+ds.orig.tar.xz.delta new file mode 100644 index 000..caf602a Binary files /dev/null and b/ariba_2.10.3+ds.orig.tar.xz.delta differ diff --git a/ariba_2.10.3+ds.orig.tar.xz.id b/ariba_2.10.3+ds.orig.tar.xz.id new file mode 100644 index 000..e7348c9 --- /dev/null +++ b/ariba_2.10.3+ds.orig.tar.xz.id @@ -0,0 +1 @@ +ef90c1926e5ac1851b9dc02f31505e8a2e6af4b0 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] annotated tag upstream/2.10.3+ds created (now 7e58752)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag upstream/2.10.3+ds in repository ariba. at 7e58752 (tag) tagging e3b0c670b51015d8351ca72e627a0245d3044d7b (commit) replaces upstream/2.10.1+ds tagged by Sascha Steinbiss on Tue Nov 28 16:59:32 2017 +0100 - Log - Upstream version 2.10.3+ds Sascha Steinbiss (1): New upstream version 2.10.3+ds --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] annotated tag debian/2.10.3+ds-1 created (now b241df1)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag debian/2.10.3+ds-1 in repository ariba. at b241df1 (tag) tagging 219815654fa9f6754d4120a7531eb4b984a67061 (commit) replaces debian/2.10.1+ds-1 tagged by Sascha Steinbiss on Wed Nov 29 10:42:55 2017 +0100 - Log - ariba Debian release 2.10.3+ds-1 -BEGIN PGP SIGNATURE- iQIzBAABCgAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAloegR8ACgkQ6NN64vCf SHIzjxAAongmNAXH8WBw8UY9/+ryRN5rmxxAWZOLo4EcikNjynkoFaLl4UvNVbtj K+C1z3aCXCoYR+Lw4zef+vlAVRTk+4nsVHF36R3nCa0cyTriG5BTcel0DuW9zL8F msNTwNz5ytNkksSpkkEr3FFDiMBhQD7R2l7Isr3GA9beVBKWyfUjmIBNZmGSXGT4 OXEPfuP6XpiZLp1lc/6rV3euiKCA4NDFnqZl2Sx2AlSOrqMB7DiC0/V0kpzHF9aI 6kY9kdqKk4aC2rzZv9iGR2wbJjk4hcgpfmqPnkO7OrLAILWp0CAHirUQR8mTmyex CQhQs2Vog0G4oW8Jk+X47QfIUHCZJdKscjwW9Wed7cP9WG6LLw+G8QwXsNMtIqzs UO3U/2caPUDE+3pf+o1/unB0CRcGzBXj2NLx24V91YgnjYcprZ3678skLaJbZrsJ vC8wVo7dJulJwJusxmTQEtdeVPGvnSoWsLjHgFHE0jkyRNKtV9clNPy4+YnK8pbo d311rIwdkXzpOFSykdA0t1x44EUi+LLPWmpv6vqYk9FFMQJwhdz2Cglp7WmoW1wA +hxNCDEWq5NQNbztLpw2kJoUxjFgLAQXUjQhY5w7jaTw5Jrmgky6SjDHfJBJ/r1h hvuFzEyFeh6WvaxFDrxag6eN+jGrolZUViQtU57dRoO4jtp1oAs= =37vO -END PGP SIGNATURE- Sascha Steinbiss (3): New upstream version 2.10.3+ds Update upstream source from tag 'upstream/2.10.3+ds' new upstream release --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] branch master updated (2198156 -> 5913b72)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch master in repository ariba. from 2198156 new upstream release new 5913b72 add d/upstream/metadata The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/changelog | 7 +++ debian/upstream/metadata | 17 + 2 files changed, 24 insertions(+) create mode 100644 debian/upstream/metadata -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] 01/01: add d/upstream/metadata
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository ariba. commit 5913b72f224de58b375657102c9127784f16dcc2 Author: Sascha Steinbiss Date: Wed Nov 29 11:21:58 2017 +0100 add d/upstream/metadata --- debian/changelog | 7 +++ debian/upstream/metadata | 17 + 2 files changed, 24 insertions(+) diff --git a/debian/changelog b/debian/changelog index e138986..00b4f3e 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +ariba (2.10.3+ds-2) UNRELEASED; urgency=medium + + * Add d/upstream/metadata. +Thanks to Steffen Moeller for providing registry information. + + -- Sascha Steinbiss Wed, 29 Nov 2017 11:21:25 +0100 + ariba (2.10.3+ds-1) unstable; urgency=medium * New upstream release. diff --git a/debian/upstream/metadata b/debian/upstream/metadata new file mode 100644 index 000..9fd7902 --- /dev/null +++ b/debian/upstream/metadata @@ -0,0 +1,17 @@ +Reference: + Author: Martin Hunt and Alison E. Mather and Leonor Sanchez-Buso and Andrew J. Page and Julian Parkhill and Jacqueline A. Keane and Simon R. Harris + Title: "ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads" + Journal: Microbial Genomics + Year: 2017 + Volume: 3 + DOI: 10.1099/mgen.0.000131 + PMID: 29177089 + URL: http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000131 + eprint: http://mgen.microbiologyresearch.org/deliver/fulltext/mgen/3/10/mgen000131.pdf?itemId=/content/journal/mgen/10.1099/mgen.0.000131&mimeType=pdf&isFastTrackArticle= +Registry: + - Name: OMICtools +Entry: OMICS_17327 + - Name: SciCrunch +Entry: NA + - Name: bio.tools +Entry: NA -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [fastaq] 01/01: pristine-tar data for fastaq_3.16.0.orig.tar.gz
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch pristine-tar in repository fastaq. commit 75fd3b0684c786538b1dfa0e7ec1cbf7240039c0 Author: Sascha Steinbiss Date: Mon Dec 4 17:53:10 2017 +0100 pristine-tar data for fastaq_3.16.0.orig.tar.gz --- fastaq_3.16.0.orig.tar.gz.delta | Bin 0 -> 7554 bytes fastaq_3.16.0.orig.tar.gz.id| 1 + 2 files changed, 1 insertion(+) diff --git a/fastaq_3.16.0.orig.tar.gz.delta b/fastaq_3.16.0.orig.tar.gz.delta new file mode 100644 index 000..fc1b9e1 Binary files /dev/null and b/fastaq_3.16.0.orig.tar.gz.delta differ diff --git a/fastaq_3.16.0.orig.tar.gz.id b/fastaq_3.16.0.orig.tar.gz.id new file mode 100644 index 000..c52dbd0 --- /dev/null +++ b/fastaq_3.16.0.orig.tar.gz.id @@ -0,0 +1 @@ +15f8ce928c931986093ddffcba61b93e94f9e376 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fastaq.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [fastaq] branch master updated (af296a2 -> ccbb92d)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch master in repository fastaq. from af296a2 Added references to registries. new c14ae5c New upstream version 3.16.0 new bf67f34 Update upstream source from tag 'upstream/3.16.0' new e8ed8a1 new upstream release new 01db3c0 bump Standards-Version new ccbb92d remove testsuite definition The 5 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: AUTHORS | 2 +- LICENSE | 4 debian/changelog| 10 -- debian/control | 3 +-- pyfastaq/tasks.py | 21 +++-- pyfastaq/tests/data/readnames_with_comments.fastq | 20 .../data/readnames_with_comments.fastq.filtered | 4 .../tests/data/readnames_with_comments.fastq.ids| 1 + pyfastaq/tests/tasks_test.py| 9 + setup.py| 4 ++-- 10 files changed, 65 insertions(+), 13 deletions(-) create mode 100644 pyfastaq/tests/data/readnames_with_comments.fastq create mode 100644 pyfastaq/tests/data/readnames_with_comments.fastq.filtered create mode 100644 pyfastaq/tests/data/readnames_with_comments.fastq.ids -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fastaq.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [fastaq] annotated tag upstream/3.16.0 created (now ef22bc8)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag upstream/3.16.0 in repository fastaq. at ef22bc8 (tag) tagging c14ae5c3e068f6aeedf4d0b41f9668851b438182 (commit) replaces upstream/3.14.0 tagged by Sascha Steinbiss on Mon Dec 4 17:53:10 2017 +0100 - Log - Upstream version 3.16.0 Sascha Steinbiss (2): New upstream version 3.15.0 New upstream version 3.16.0 --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fastaq.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [fastaq] 05/05: remove testsuite definition
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository fastaq. commit ccbb92dfb5122196c131da85bdd6020a7fd3b6a5 Author: Sascha Steinbiss Date: Mon Dec 4 19:00:12 2017 +0100 remove testsuite definition --- debian/changelog | 1 + debian/control | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index 091135e..5b0273f 100644 --- a/debian/changelog +++ b/debian/changelog @@ -7,6 +7,7 @@ fastaq (3.16.0-1) unstable; urgency=medium [ Sascha Steinbiss ] * New upstream release. * Bump Standards-Version. + * Remove unnecessary Testsuite: entry in d/control. -- Sascha Steinbiss Mon, 04 Dec 2017 17:53:43 +0100 diff --git a/debian/control b/debian/control index 68cf83d..7663897 100644 --- a/debian/control +++ b/debian/control @@ -5,7 +5,6 @@ Uploaders: Andreas Tille , Sascha Steinbiss Section: science Priority: optional -Testsuite: autopkgtest Build-Depends: debhelper (>= 9), dh-python, python3, -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fastaq.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [fastaq] annotated tag debian/3.16.0-1 created (now 2882363)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag debian/3.16.0-1 in repository fastaq. at 2882363 (tag) tagging ccbb92dfb5122196c131da85bdd6020a7fd3b6a5 (commit) replaces debian/3.15.0-2 tagged by Sascha Steinbiss on Tue Dec 5 00:49:55 2017 +0100 - Log - fastaq Debian release 3.16.0-1 -BEGIN PGP SIGNATURE- iQIzBAABCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAlol3yMACgkQ6NN64vCf SHKLzQ//VsHPHPoENTyrCM6tOXj2b70DljwulbZUAnk1TPDF2tqHLxwqLVd1RdYb 3P7vQkyjV+6+7RbKpdojduOM1s/wYA6z2y3y+PXe97/jNs8V3iTmNxLyYOI5aPiA Gt5mlF8V/QWrUTKRMDuOk7ilIoAuPD4gasouILrn5IQm6vu7e8xadFJDDkj3qqsJ QkK8ByPkAXnIUhH7ib/KehWOlseoS3eODwFGNWSgbJDLimM999PcAaJRgFrl9NK6 xOxaTVicgwSbrJds5s9+YIc7n+IuAEq2qzASpaYQS4+2ztZdxFihB0kmtHqVH9Mh QUSsuKQA6j/uzjE1ZOOuiKHplEa2rCVep4umoEm7hLSvmdCzuzjGua67uV11gu3L HYiDpWLkJhtKqBfLai4NfWmua+KRU7DSX4YR36WFszEslOjlKeUOimBg//Bx47+h ilNG1qfqYVeouST7JTmrgvK8mp/vYxRH5JOwUCL5+r7juYxfuhoVapYOgmwVNZCV +q/4ZCBExV5ZixZK54rJLq+t9uCOKZGYYMSs2KQF4HNAAYWwSnpHQ8pNymjCdye8 OohUin6JsKJZGuRvKkvxbyiR8ZdRtGPL5G2hlC1xYHbrFn3YAdD6+L1WwHTHaxc4 ir2wSwYmAvz+QHCSJvYxbmSMWwUEZaXIIoXs7W0EwSWuWLWna+A= =xYdV -END PGP SIGNATURE- Sascha Steinbiss (5): New upstream version 3.16.0 Update upstream source from tag 'upstream/3.16.0' new upstream release bump Standards-Version remove testsuite definition Steffen Moeller (1): Added references to registries. --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fastaq.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [fastaq] 01/05: New upstream version 3.16.0
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository fastaq.
commit c14ae5c3e068f6aeedf4d0b41f9668851b438182
Author: Sascha Steinbiss
Date: Mon Dec 4 17:53:09 2017 +0100
New upstream version 3.16.0
---
AUTHORS | 2 +-
LICENSE | 4
pyfastaq/tasks.py | 21 +++--
pyfastaq/tests/data/readnames_with_comments.fastq | 20
.../data/readnames_with_comments.fastq.filtered | 4
.../tests/data/readnames_with_comments.fastq.ids| 1 +
pyfastaq/tests/tasks_test.py| 9 +
setup.py| 4 ++--
8 files changed, 56 insertions(+), 9 deletions(-)
diff --git a/AUTHORS b/AUTHORS
index 711ae85..39205dc 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -1 +1 @@
-Martin Hunt (m...@sanger.ac.uk)
+Martin Hunt (path-h...@sanger.ac.uk)
diff --git a/LICENSE b/LICENSE
index 1a0079f..8e19ad1 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,3 +1,7 @@
+Copyright (c) 2013 - 2017 by Genome Research Ltd.
+
+This is free software, licensed under:
+
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
diff --git a/pyfastaq/tasks.py b/pyfastaq/tasks.py
index b788672..f5e1c52 100644
--- a/pyfastaq/tasks.py
+++ b/pyfastaq/tasks.py
@@ -306,13 +306,22 @@ def filter(
r = re.compile(regex)
-def passes(seq):
+def passes(seq, name_regex):
+# remove trailing comments from FASTQ readname lines
+matches = name_regex.match(seq.id)
+if matches is not None:
+clean_seq_id = matches.group(1)
+else:
+clean_seq_id = seq.id
+
return minlength <= len(seq) <= maxlength \
- and (regex is None or r.search(seq.id) is not None) \
- and (ids_file is None or seq.id in ids_from_file)
-
+ and (regex is None or r.search(clean_seq_id) is not None) \
+ and (ids_file is None or clean_seq_id in ids_from_file)
+
+name_regex = re.compile(r'^([^\s]+).*?$')
+
for seq in seq_reader:
-seq_passes = passes(seq)
+seq_passes = passes(seq, name_regex)
if mate_in:
try:
seq_mate = next(seq_reader_mate)
@@ -320,7 +329,7 @@ def filter(
utils.close(f_out)
raise Error('Error getting mate for sequence', seq.id, ' ...
cannot continue')
-mate_passes = passes(seq_mate)
+mate_passes = passes(seq_mate, name_regex)
want_the_pair = (seq_passes and mate_passes) \
or (( seq_passes or mate_passes) and not
both_mates_pass)
if want_the_pair != invert:
diff --git a/pyfastaq/tests/data/readnames_with_comments.fastq
b/pyfastaq/tests/data/readnames_with_comments.fastq
new file mode 100644
index 000..8adbb17
--- /dev/null
+++ b/pyfastaq/tests/data/readnames_with_comments.fastq
@@ -0,0 +1,20 @@
+@A1234::15950:1663 stuff_to_remove
+TCGTAAGCCTGCTCGAGC
++
+>>3>>44@CFFFGG??EE
+@A1234::16080:1672 stuff_to_remove
+CCATCGTCTTCGCCCTGC
++
+111AA1F1EAEGAG
+@A1234::12967:1677 stuff_to_remove
+CTCCAGCATCGTGCAAAT
++
+3>>A?@CBDFAAACCBAF
+@A1234::16114:1681 stuff_to_remove
+TTGATATAGAGATACTTC
++
+3>A3A5D55DBFFDFGGG
+@A1234::16669:1683 stuff_to_remove
+CTGCGCGACTATACGCAG
++
+1>1>>>A1>D?FF10E0A
\ No newline at end of file
diff --git a/pyfastaq/tests/data/readnames_with_comments.fastq.filtered
b/pyfastaq/tests/data/readnames_with_comments.fastq.filtered
new file mode 100644
index 000..f277d15
--- /dev/null
+++ b/pyfastaq/tests/data/readnames_with_comments.fastq.filtered
@@ -0,0 +1,4 @@
+@A1234::12967:1677 stuff_to_remove
+CTCCAGCATCGTGCAAAT
++
+3>>A?@CBDFAAACCBAF
diff --git a/pyfastaq/tests/data/readnames_with_comments.fastq.ids
b/pyfastaq/tests/data/readnames_with_comments.fastq.ids
new file mode 100644
index 000..9343080
--- /dev/null
+++ b/pyfastaq/tests/data/readnames_with_comments.fastq.ids
@@ -0,0 +1 @@
+A1234::12967:1677
\ No newline at end of file
diff --git a/pyfastaq/tests/tasks_test.py b/pyfastaq/tests/tasks_test.py
index 5db41d4..a8856bb 100644
--- a/pyfastaq/tests/tasks_test.py
+++ b/pyfastaq/tests/tasks_test.py
@@ -179,6 +179,14 @@ class TestFilter(unittest.TestCase):
tasks.filter(infile, outfile, ids_file=infile + '.ids')
self.assertTrue(filecmp.cmp(infile + '.filtered', outfile))
os.unlink(outfile)
+
+def test_ids_with_comments_from_file_filter(self):
+'''Test that can extract reads from a file of read names where the
read names have extra data after space'''
+infile = os.path.join(data_dir, 'readnames_with_comments.fastq'
[med-svn] [fastaq] 03/05: new upstream release
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository fastaq. commit e8ed8a156b489de324eefb8ef1e5983c9489c88a Author: Sascha Steinbiss Date: Mon Dec 4 17:56:06 2017 +0100 new upstream release --- debian/changelog | 8 ++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/debian/changelog b/debian/changelog index d88ffd4..530789b 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,9 +1,13 @@ -fastaq (3.15.0-2) UNRELEASED; urgency=medium +fastaq (3.16.0-1) unstable; urgency=medium + [ Steffen Moeller ] * debian/upstream/metadata: Added references to registries. - -- Steffen Moeller Sat, 16 Sep 2017 03:47:49 +0200 + [ Sascha Steinbiss ] + * New upstream release. + + -- Sascha Steinbiss Mon, 04 Dec 2017 17:53:43 +0100 fastaq (3.15.0-2) unstable; urgency=medium -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fastaq.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [fastaq] branch pristine-tar updated (db463b3 -> 75fd3b0)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch pristine-tar in repository fastaq. from db463b3 pristine-tar data for fastaq_3.15.0.orig.tar.gz new 75fd3b0 pristine-tar data for fastaq_3.16.0.orig.tar.gz The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: fastaq_3.16.0.orig.tar.gz.delta | Bin 0 -> 7554 bytes fastaq_3.16.0.orig.tar.gz.id| 1 + 2 files changed, 1 insertion(+) create mode 100644 fastaq_3.16.0.orig.tar.gz.delta create mode 100644 fastaq_3.16.0.orig.tar.gz.id -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fastaq.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [fastaq] 02/05: Update upstream source from tag 'upstream/3.16.0'
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository fastaq. commit bf67f345132638b9dd8b4f01e10003b2d0fd14aa Merge: af296a2 c14ae5c Author: Sascha Steinbiss Date: Mon Dec 4 17:53:11 2017 +0100 Update upstream source from tag 'upstream/3.16.0' Update to upstream version '3.16.0' with Debian dir bea3e795a52a14ea2532649b463db31230289117 AUTHORS | 2 +- LICENSE | 4 pyfastaq/tasks.py | 21 +++-- pyfastaq/tests/data/readnames_with_comments.fastq | 20 .../data/readnames_with_comments.fastq.filtered | 4 .../tests/data/readnames_with_comments.fastq.ids| 1 + pyfastaq/tests/tasks_test.py| 9 + setup.py| 4 ++-- 8 files changed, 56 insertions(+), 9 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fastaq.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [fastaq] branch upstream updated (3a28586 -> c14ae5c)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch upstream in repository fastaq. from 3a28586 New upstream version 3.15.0 new c14ae5c New upstream version 3.16.0 The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: AUTHORS | 2 +- LICENSE | 4 pyfastaq/tasks.py | 21 +++-- pyfastaq/tests/data/readnames_with_comments.fastq | 20 .../data/readnames_with_comments.fastq.filtered | 4 .../tests/data/readnames_with_comments.fastq.ids| 1 + pyfastaq/tests/tasks_test.py| 9 + setup.py| 4 ++-- 8 files changed, 56 insertions(+), 9 deletions(-) create mode 100644 pyfastaq/tests/data/readnames_with_comments.fastq create mode 100644 pyfastaq/tests/data/readnames_with_comments.fastq.filtered create mode 100644 pyfastaq/tests/data/readnames_with_comments.fastq.ids -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fastaq.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [fastaq] 04/05: bump Standards-Version
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository fastaq. commit 01db3c0918a0adee76f2c48a0be93ce844e27b0f Author: Sascha Steinbiss Date: Mon Dec 4 17:56:35 2017 +0100 bump Standards-Version --- debian/changelog | 1 + debian/control | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index 530789b..091135e 100644 --- a/debian/changelog +++ b/debian/changelog @@ -6,6 +6,7 @@ fastaq (3.16.0-1) unstable; urgency=medium [ Sascha Steinbiss ] * New upstream release. + * Bump Standards-Version. -- Sascha Steinbiss Mon, 04 Dec 2017 17:53:43 +0100 diff --git a/debian/control b/debian/control index 5e89390..68cf83d 100644 --- a/debian/control +++ b/debian/control @@ -15,7 +15,7 @@ Build-Depends: debhelper (>= 9), samtools, help2man X-Python3-Version: >= 3.2 -Standards-Version: 3.9.8 +Standards-Version: 4.1.1 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/fastaq.git Vcs-Git: https://anonscm.debian.org/git/debian-med/fastaq.git Homepage: https://github.com/sanger-pathogens/Fastaq -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fastaq.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/codonw] Pushed new tag debian/1.4.4-5
Sascha Steinbiss pushed new tag debian/1.4.4-5 at Debian Med / codonw -- View it on GitLab: https://salsa.debian.org/med-team/codonw/-/tree/debian/1.4.4-5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/codonw][master] 2 commits: upload to unstable
Sascha Steinbiss pushed to branch master at Debian Med / codonw Commits: b63b22d2 by Sascha Steinbiss at 2020-05-16T07:22:46+02:00 upload to unstable - - - - - f000b782 by Sascha Steinbiss at 2020-05-16T07:24:37+02:00 mention autopkgtest in d/changelog - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = @@ -1,4 +1,4 @@ -codonw (1.4.4-5) UNRELEASED; urgency=medium +codonw (1.4.4-5) unstable; urgency=medium * Team Upload. @@ -11,6 +11,7 @@ codonw (1.4.4-5) UNRELEASED; urgency=medium * Add salsa-ci file (routine-update) * routine-update: Add salsa-ci file * Add "Rules-Requires-Root:no" + * Add autopkgtest. -- Nilesh Patra Fri, 15 May 2020 22:47:57 +0530 View it on GitLab: https://salsa.debian.org/med-team/codonw/-/compare/57f4b338d4d5aa56a6947f57e29a71062b2695cd...f000b782de5c2275a48614e184418fb22438f3ee -- View it on GitLab: https://salsa.debian.org/med-team/codonw/-/compare/57f4b338d4d5aa56a6947f57e29a71062b2695cd...f000b782de5c2275a48614e184418fb22438f3ee You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ariba] Pushed new tag debian/2.14.5+ds-1
Sascha Steinbiss pushed new tag debian/2.14.5+ds-1 at Debian Med / ariba -- View it on GitLab: https://salsa.debian.org/med-team/ariba/-/tree/debian/2.14.5+ds-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ariba] Pushed new tag upstream/2.14.5+ds
Sascha Steinbiss pushed new tag upstream/2.14.5+ds at Debian Med / ariba -- View it on GitLab: https://salsa.debian.org/med-team/ariba/-/tree/upstream/2.14.5+ds You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ariba][pristine-tar] pristine-tar data for ariba_2.14.5+ds.orig.tar.xz
Sascha Steinbiss pushed to branch pristine-tar at Debian Med / ariba Commits: fe35a6a3 by Sascha Steinbiss at 2020-05-21T19:18:24+02:00 pristine-tar data for ariba_2.14.5+ds.orig.tar.xz - - - - - 2 changed files: - + ariba_2.14.5+ds.orig.tar.xz.delta - + ariba_2.14.5+ds.orig.tar.xz.id Changes: = ariba_2.14.5+ds.orig.tar.xz.delta = Binary files /dev/null and b/ariba_2.14.5+ds.orig.tar.xz.delta differ = ariba_2.14.5+ds.orig.tar.xz.id = @@ -0,0 +1 @@ +134eec6a4736d3caf8a20ba32d660467bd00f6f5 View it on GitLab: https://salsa.debian.org/med-team/ariba/-/commit/fe35a6a310514b8d209b0be12fc1a440f3f7184b -- View it on GitLab: https://salsa.debian.org/med-team/ariba/-/commit/fe35a6a310514b8d209b0be12fc1a440f3f7184b You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/gfapy][pristine-tar] pristine-tar data for gfapy_1.1.0+dfsg.orig.tar.xz
Sascha Steinbiss pushed to branch pristine-tar at Debian Med / gfapy Commits: de4689a9 by Sascha Steinbiss at 2020-05-30T17:42:16+02:00 pristine-tar data for gfapy_1.1.0+dfsg.orig.tar.xz - - - - - 2 changed files: - + gfapy_1.1.0+dfsg.orig.tar.xz.delta - + gfapy_1.1.0+dfsg.orig.tar.xz.id Changes: = gfapy_1.1.0+dfsg.orig.tar.xz.delta = Binary files /dev/null and b/gfapy_1.1.0+dfsg.orig.tar.xz.delta differ = gfapy_1.1.0+dfsg.orig.tar.xz.id = @@ -0,0 +1 @@ +62a7271b8f7eb1367ff9d271904a7e988328950c View it on GitLab: https://salsa.debian.org/med-team/gfapy/-/commit/de4689a9ef2e404043931458d3d3cdb15507149a -- View it on GitLab: https://salsa.debian.org/med-team/gfapy/-/commit/de4689a9ef2e404043931458d3d3cdb15507149a You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/gfapy][master] 6 commits: New upstream version 1.1.0+dfsg
Sascha Steinbiss pushed to branch master at Debian Med / gfapy Commits: e9dda158 by Sascha Steinbiss at 2020-05-30T17:42:15+02:00 New upstream version 1.1.0+dfsg - - - - - 7b933c9d by Sascha Steinbiss at 2020-05-30T17:42:16+02:00 Update upstream source from tag 'upstream/1.1.0+dfsg' Update to upstream version '1.1.0+dfsg' with Debian dir f4e65cb2228aa295ac06db0176433ee8e0c066e0 - - - - - 77105f85 by Sascha Steinbiss at 2020-05-30T22:53:23+02:00 new upstream release - - - - - 39215dad by Sascha Steinbiss at 2020-05-30T22:53:40+02:00 use debhelper 13 - - - - - 4d6eb610 by Sascha Steinbiss at 2020-05-30T22:53:52+02:00 update d/changelog - - - - - 7b074a89 by Sascha Steinbiss at 2020-05-30T22:54:07+02:00 bump Standards-Version - - - - - 30 changed files: - CHANGES.txt - Makefile - README.rst - + bin/gfapy-renumber - debian/changelog - debian/control - doc/conf.py - doc/index.rst - doc/tutorial/alignments.rst - doc/tutorial/comments.rst - doc/tutorial/custom_records.rst - doc/tutorial/gfa.rst - doc/tutorial/header.rst - doc/tutorial/positional_fields.rst - doc/tutorial/references.rst - + doc/tutorial/rgfa.rst - doc/tutorial/tags.rst - doc/tutorial/validation.rst - gfapy/__init__.py - gfapy/field/parser.py - gfapy/gfa.py - gfapy/line/common/construction.py - gfapy/line/common/field_data.py - gfapy/line/common/validate.py - gfapy/line/common/version_conversion.py - gfapy/line/common/writer.py - gfapy/line/line.py - gfapy/lines/creators.py - + gfapy/rgfa.py - setup.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/gfapy/-/compare/518bd3f0d1af0b69da699d27b9495b21d8e5e9f9...7b074a8964d8ee12a896a70e9e4ce3e606458fee -- View it on GitLab: https://salsa.debian.org/med-team/gfapy/-/compare/518bd3f0d1af0b69da699d27b9495b21d8e5e9f9...7b074a8964d8ee12a896a70e9e4ce3e606458fee You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/gfapy] Pushed new tag upstream/1.1.0+dfsg
Sascha Steinbiss pushed new tag upstream/1.1.0+dfsg at Debian Med / gfapy -- View it on GitLab: https://salsa.debian.org/med-team/gfapy/-/tree/upstream/1.1.0+dfsg You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/gfapy][upstream] New upstream version 1.1.0+dfsg
Sascha Steinbiss pushed to branch upstream at Debian Med / gfapy Commits: e9dda158 by Sascha Steinbiss at 2020-05-30T17:42:15+02:00 New upstream version 1.1.0+dfsg - - - - - 30 changed files: - CHANGES.txt - Makefile - README.rst - + bin/gfapy-renumber - doc/conf.py - doc/index.rst - doc/tutorial/alignments.rst - doc/tutorial/comments.rst - doc/tutorial/custom_records.rst - doc/tutorial/gfa.rst - doc/tutorial/header.rst - doc/tutorial/positional_fields.rst - doc/tutorial/references.rst - + doc/tutorial/rgfa.rst - doc/tutorial/tags.rst - doc/tutorial/validation.rst - gfapy/__init__.py - gfapy/field/parser.py - gfapy/gfa.py - gfapy/line/common/construction.py - gfapy/line/common/field_data.py - gfapy/line/common/validate.py - gfapy/line/common/version_conversion.py - gfapy/line/common/writer.py - gfapy/line/line.py - gfapy/lines/creators.py - + gfapy/rgfa.py - setup.py - + tests/test_api_rgfa.py - tests/test_api_tags.py The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/gfapy/-/commit/e9dda158ab2ff116f026efb8d2f89908c754c6d5 -- View it on GitLab: https://salsa.debian.org/med-team/gfapy/-/commit/e9dda158ab2ff116f026efb8d2f89908c754c6d5 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/gfapy] Pushed new tag debian/1.1.0+dfsg-1
Sascha Steinbiss pushed new tag debian/1.1.0+dfsg-1 at Debian Med / gfapy -- View it on GitLab: https://salsa.debian.org/med-team/gfapy/-/tree/debian/1.1.0+dfsg-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ariba] Pushed new tag debian/2.14.5+ds-2
Sascha Steinbiss pushed new tag debian/2.14.5+ds-2 at Debian Med / ariba -- View it on GitLab: https://salsa.debian.org/med-team/ariba/-/tree/debian/2.14.5+ds-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ariba] Pushed new tag debian/2.14.5+ds-3
Sascha Steinbiss pushed new tag debian/2.14.5+ds-3 at Debian Med / ariba -- View it on GitLab: https://salsa.debian.org/med-team/ariba/-/tree/debian/2.14.5+ds-3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ariba][master] only build-depend on spades on amd64
Sascha Steinbiss pushed to branch master at Debian Med / ariba Commits: e2ed8ac0 by Sascha Steinbiss at 2020-07-05T12:40:55+02:00 only build-depend on spades on amd64 - - - - - 2 changed files: - debian/changelog - debian/control Changes: = debian/changelog = @@ -1,3 +1,9 @@ +ariba (2.14.5+ds-3) unstable; urgency=medium + + * Only build-depend on spades on amd64. + + -- Sascha Steinbiss Fri, 03 Jul 2020 19:55:45 +0200 + ariba (2.14.5+ds-2) unstable; urgency=medium [ Andreas Tille ] = debian/control = @@ -24,7 +24,7 @@ Build-Depends: debhelper-compat (= 13), fastaq (>= 3.12.0), help2man, asciidoctor, - spades + spades [amd64] Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/ariba Vcs-Git: https://salsa.debian.org/med-team/ariba.git View it on GitLab: https://salsa.debian.org/med-team/ariba/-/commit/e2ed8ac021b503644386e17aa075c6aef13ba79d -- View it on GitLab: https://salsa.debian.org/med-team/ariba/-/commit/e2ed8ac021b503644386e17aa075c6aef13ba79d You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools][master] add patch to fix build on GCC10
Sascha Steinbiss pushed to branch master at Debian Med / genometools
Commits:
bb3bf8ab by Sascha Steinbiss at 2020-07-22T13:33:29+02:00
add patch to fix build on GCC10
- - - - -
4 changed files:
- debian/changelog
- debian/patches/adding_soname
- + debian/patches/gcc10.patch
- debian/patches/series
Changes:
=
debian/changelog
=
@@ -1,3 +1,10 @@
+genometools (1.6.1+ds-3) unstable; urgency=medium
+
+ * Add patch to fix build on GCC 10.
+Closes: #957268
+
+ -- Sascha Steinbiss Wed, 22 Jul 2020 13:00:06 +0200
+
genometools (1.6.1+ds-2) unstable; urgency=medium
* Use static images for AnnotationSketch documentation.
=
debian/patches/adding_soname
=
@@ -25,7 +25,7 @@ Author: Sascha Steinbiss
define PROGRAM_template
$(1): $(2)
-@@ -1003,7 +1005,8 @@
+@@ -999,7 +1001,8 @@
$(RANLIB) $(prefix)/lib/libgenometools.a
endif
ifneq ($(sharedlib),no)
=
debian/patches/gcc10.patch
=
@@ -0,0 +1,88 @@
+From 51205942b1f41abdf841771deac4e0e35d7d5016 Mon Sep 17 00:00:00 2001
+From: Sascha Steinbiss
+Date: Wed, 22 Apr 2020 21:59:57 +0200
+Subject: [PATCH 1/2] make sure to not ignore snprintf output
+
+GCC 10 will warn about the (here intended) silent string truncation
+done by snprintf() unless the return value is handled.
+Obviously this will break the build as we use -Werror. We
+circumvent the problem by checking the output value and printing a
+warning if we notice a truncation.
+---
+ src/ltr/ltrdigest_file_out_stream.c | 17 -
+ 1 file changed, 12 insertions(+), 5 deletions(-)
+
+diff --git a/src/ltr/ltrdigest_file_out_stream.c
b/src/ltr/ltrdigest_file_out_stream.c
+index 723b8cf9a..61325b693 100644
+--- a/src/ltr/ltrdigest_file_out_stream.c
b/src/ltr/ltrdigest_file_out_stream.c
+@@ -1,5 +1,5 @@
+ /*
+- Copyright (c) 2008-2015 Sascha Steinbiss
++ Copyright (c) 2008-2020 Sascha Steinbiss
+ Copyright (c) 2008-2013 Center for Bioinformatics, University of Hamburg
+
+ Permission to use, copy, modify, and distribute this software for any
+@@ -33,6 +33,7 @@
+ #include "core/symbol.h"
+ #include "core/undef_api.h"
+ #include "core/unused_api.h"
++#include "core/warning_api.h"
+ #include "extended/extract_feature_sequence.h"
+ #include "extended/feature_node.h"
+ #include "extended/feature_node_iterator_api.h"
+@@ -416,6 +417,8 @@ int gt_ltrfileout_stream_next(GtNodeStream *ns,
GtGenomeNode **gn, GtError *err)
+
+ if (!had_err) {
+ GtRange rng;
++ int ret = 0;
++
+ ls->element.seqid = gt_calloc((size_t) ls->seqnamelen+1, sizeof (char));
+ (void) snprintf(ls->element.seqid,
+ GT_MIN((size_t) gt_str_length(sdesc),
+@@ -425,12 +428,16 @@ int gt_ltrfileout_stream_next(GtNodeStream *ns,
GtGenomeNode **gn, GtError *err)
+ if (gt_str_length(sdesc) > (GtUword) ls->seqnamelen)
+ ls->element.seqid[ls->seqnamelen] = '\0';
+
+- (void) gt_ltrelement_format_description(&ls->element,
+- ls->seqnamelen,
+- desc,
+- (size_t) (GT_MAXFASTAHEADER-1));
++ ret = gt_ltrelement_format_description(&ls->element,
++ ls->seqnamelen,
++ desc,
++ (size_t) (GT_MAXFASTAHEADER-1));
++ if (ret < 0) {
++gt_warning("FASTA header truncated: %s", desc);
++ }
+ gt_str_delete(sdesc);
+
++
+ /* output basic retrotransposon data */
+ lltr_rng = gt_genome_node_get_range((GtGenomeNode*)
ls->element.leftLTR);
+ rltr_rng = gt_genome_node_get_range((GtGenomeNode*)
ls->element.rightLTR);
+
+From 30ae36037228dc4ed174e8462f3489638e6f5e76 Mon Sep 17 00:00:00 2001
+From: Sascha Steinbiss
+Date: Wed, 22 Apr 2020 22:01:00 +0200
+Subject: [PATCH 2/2] declare hashmap type as extern
+
+This fixes a build issue with GCC 10.
+Closes #941.
+---
+ src/mgth/metagenomethreader.h | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/mgth/metagenomethreader.h b/src/mgth/metagenomethreader.h
+index 92f16d498..7f76fffb9 100644
+--- a/src/mgth/metagenomethreader.h
b/src/mgth/metagenomethreader.h
+@@ -221,7 +221,7 @@ typedef struct
+ } ParseStruct;
+
+ /* specific access mode of queryhash */
+-DECLARE_HASHMAP(char *, gt_cstr_nofree, GtUword *, ulp,,)
++DECLARE_HASHMAP(char *, gt_cstr_nofree, GtUword *, ulp, extern,)
+ DECLARE_SAFE_DEREF(GtUword *, ulp)
+
+ /* Funktion, mit der der Metagenomethreader gestartet wird
=
debi
[med-svn] [Git][med-team/genometools] Pushed new tag debian/1.6.1+ds-3_bpo10+1
Sascha Steinbiss pushed new tag debian/1.6.1+ds-3_bpo10+1 at Debian Med / genometools -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/tree/debian/1.6.1+ds-3_bpo10+1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ariba] Pushed new tag debian/2.14.6+ds-1
Sascha Steinbiss pushed new tag debian/2.14.6+ds-1 at Debian Med / ariba -- View it on GitLab: https://salsa.debian.org/med-team/ariba/-/tree/debian/2.14.6+ds-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ariba] Pushed new tag upstream/2.14.6+ds
Sascha Steinbiss pushed new tag upstream/2.14.6+ds at Debian Med / ariba -- View it on GitLab: https://salsa.debian.org/med-team/ariba/-/tree/upstream/2.14.6+ds You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ariba][pristine-tar] pristine-tar data for ariba_2.14.6+ds.orig.tar.xz
Sascha Steinbiss pushed to branch pristine-tar at Debian Med / ariba Commits: 896d9c39 by Sascha Steinbiss at 2020-09-13T18:30:35+02:00 pristine-tar data for ariba_2.14.6+ds.orig.tar.xz - - - - - 2 changed files: - + ariba_2.14.6+ds.orig.tar.xz.delta - + ariba_2.14.6+ds.orig.tar.xz.id Changes: = ariba_2.14.6+ds.orig.tar.xz.delta = Binary files /dev/null and b/ariba_2.14.6+ds.orig.tar.xz.delta differ = ariba_2.14.6+ds.orig.tar.xz.id = @@ -0,0 +1 @@ +e6770ca977d8939e9d04528617c6e33b7c15c372 View it on GitLab: https://salsa.debian.org/med-team/ariba/-/commit/896d9c391b2a62fa5df9bfb0d0e487faf935affd -- View it on GitLab: https://salsa.debian.org/med-team/ariba/-/commit/896d9c391b2a62fa5df9bfb0d0e487faf935affd You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/ariba][master] 3 commits: New upstream version 2.14.6+ds
Sascha Steinbiss pushed to branch master at Debian Med / ariba
Commits:
65895acf by Sascha Steinbiss at 2020-09-13T18:30:27+02:00
New upstream version 2.14.6+ds
- - - - -
6c13d984 by Sascha Steinbiss at 2020-09-13T18:30:35+02:00
Update upstream source from tag 'upstream/2.14.6+ds'
Update to upstream version '2.14.6+ds'
with Debian dir 68512f1670550c5c2eb3ec3908e5b16ad93ed131
- - - - -
280aced8 by Sascha Steinbiss at 2020-09-14T08:56:47+02:00
new upstream release
- - - - -
6 changed files:
- CHANGELOG.md
- ariba/pubmlst_getter.py
- ariba/ref_genes_getter.py
- debian/changelog
- debian/patches/add-testdata.patch
- setup.py
Changes:
=
CHANGELOG.md
=
@@ -1,5 +1,20 @@
# Change Log
+## [v2.14.6](https://github.com/sanger-pathogens/ariba/tree/v2.14.6)
(2020-09-07)
+[Full
Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.5...v2.14.6)
+
+**Closed issues:**
+
+- PubMLST URL change breaks pubmlstget
[\#304](https://github.com/sanger-pathogens/ariba/issues/304)
+- get\_ref card is attempting to download RGI
[\#301](https://github.com/sanger-pathogens/ariba/issues/301)
+- Reference dataset of megares cannot be downloaded
[\#287](https://github.com/sanger-pathogens/ariba/issues/287)
+
+**Merged pull requests:**
+
+- Fix for changes in PubMLST url
[\#305](https://github.com/sanger-pathogens/ariba/pull/305)
([rpetit3](https://github.com/rpetit3))
+- Solution 1: for fixing CARD download
[\#302](https://github.com/sanger-pathogens/ariba/pull/302)
([rpetit3](https://github.com/rpetit3))
+- Update CARD citation message
[\#289](https://github.com/sanger-pathogens/ariba/pull/289)
([fmaguire](https://github.com/fmaguire))
+
## [v2.14.5](https://github.com/sanger-pathogens/ariba/tree/v2.14.5)
(2020-05-14)
[Full
Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.4...v2.14.5)
=
ariba/pubmlst_getter.py
=
@@ -105,7 +105,7 @@ class PubmlstGetter:
self._download_file(profile_url, profile_outfile)
for fasta_url in fasta_urls:
-outfile = os.path.join(outdir, fasta_url.split('/')[-1])
+outfile = "{0}.tfa".format(os.path.join(outdir,
fasta_url.split('/')[-2]))
self._download_file(fasta_url, outfile + '.tmp')
PubmlstGetter._rename_seqs_in_fasta(outfile + '.tmp', outfile)
os.unlink(outfile + '.tmp')
=
ariba/ref_genes_getter.py
=
@@ -42,7 +42,7 @@ class RefGenesGetter:
def _get_card_versions(self, tmp_file):
print('Getting available CARD versions')
common.download_file('https://card.mcmaster.ca/download', tmp_file,
max_attempts=self.max_download_attempts, sleep_time=self.sleep_time,
verbose=True)
-p =
re.compile(r'''href="(/download/.*?broad.*?v([0-9]+\.[0-9]+\.[0-9]+)\.tar\.(gz|bz2))"''')
+p =
re.compile(r'''href="(/download/0/.*?broad.*?v([0-9]+\.[0-9]+\.[0-9]+)\.tar\.(gz|bz2))"''')
versions = {}
with open(tmp_file) as f:
@@ -183,7 +183,7 @@ class RefGenesGetter:
print('You can use them with ARIBA like this:')
print('ariba prepareref -f', final_fasta, '-m', final_tsv,
'output_directory\n')
print('If you use this downloaded data, please cite:')
-print('"The Comprehensive Antibiotic Resistance Database", McArthur et
al 2013, PMID: 23650175')
+print('"CARD 2020: antibiotic resistome surveillance with the
comprehensive antibiotic resistance database", Alcock et al 2020, PMID:
31665441')
print('and in your methods say that version', self.version, 'of the
database was used')
@@ -659,6 +659,6 @@ class RefGenesGetter:
print('ariba prepareref -f', final_fasta, '-m',
final_tsv, 'output_directory\n')
else:
-print(f"Nothing to do. Exiting.")
+ print(f"Nothing to do. Exiting.")
def run(self, outprefix):
exec('self._get_from_' + self.ref_db + '(outprefix)')
=
debian/changelog
=
@@ -1,3 +1,9 @@
+ariba (2.14.6+ds-1) unstable; urgency=medium
+
+ * New upstream release.
+
+ -- Sascha Steinbiss Sun, 13 Sep 2020 18:34:46 +0200
+
ariba (2.14.5+ds-3) unstable; urgency=medium
* Only build-depend on spades on amd64.
=
debian/patches/add-testdata.patch
=
@@
[med-svn] [Git][med-team/ariba][upstream] New upstream version 2.14.6+ds
Sascha Steinbiss pushed to branch upstream at Debian Med / ariba
Commits:
65895acf by Sascha Steinbiss at 2020-09-13T18:30:27+02:00
New upstream version 2.14.6+ds
- - - - -
4 changed files:
- CHANGELOG.md
- ariba/pubmlst_getter.py
- ariba/ref_genes_getter.py
- setup.py
Changes:
=
CHANGELOG.md
=
@@ -1,5 +1,20 @@
# Change Log
+## [v2.14.6](https://github.com/sanger-pathogens/ariba/tree/v2.14.6)
(2020-09-07)
+[Full
Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.5...v2.14.6)
+
+**Closed issues:**
+
+- PubMLST URL change breaks pubmlstget
[\#304](https://github.com/sanger-pathogens/ariba/issues/304)
+- get\_ref card is attempting to download RGI
[\#301](https://github.com/sanger-pathogens/ariba/issues/301)
+- Reference dataset of megares cannot be downloaded
[\#287](https://github.com/sanger-pathogens/ariba/issues/287)
+
+**Merged pull requests:**
+
+- Fix for changes in PubMLST url
[\#305](https://github.com/sanger-pathogens/ariba/pull/305)
([rpetit3](https://github.com/rpetit3))
+- Solution 1: for fixing CARD download
[\#302](https://github.com/sanger-pathogens/ariba/pull/302)
([rpetit3](https://github.com/rpetit3))
+- Update CARD citation message
[\#289](https://github.com/sanger-pathogens/ariba/pull/289)
([fmaguire](https://github.com/fmaguire))
+
## [v2.14.5](https://github.com/sanger-pathogens/ariba/tree/v2.14.5)
(2020-05-14)
[Full
Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.4...v2.14.5)
=
ariba/pubmlst_getter.py
=
@@ -105,7 +105,7 @@ class PubmlstGetter:
self._download_file(profile_url, profile_outfile)
for fasta_url in fasta_urls:
-outfile = os.path.join(outdir, fasta_url.split('/')[-1])
+outfile = "{0}.tfa".format(os.path.join(outdir,
fasta_url.split('/')[-2]))
self._download_file(fasta_url, outfile + '.tmp')
PubmlstGetter._rename_seqs_in_fasta(outfile + '.tmp', outfile)
os.unlink(outfile + '.tmp')
=
ariba/ref_genes_getter.py
=
@@ -42,7 +42,7 @@ class RefGenesGetter:
def _get_card_versions(self, tmp_file):
print('Getting available CARD versions')
common.download_file('https://card.mcmaster.ca/download', tmp_file,
max_attempts=self.max_download_attempts, sleep_time=self.sleep_time,
verbose=True)
-p =
re.compile(r'''href="(/download/.*?broad.*?v([0-9]+\.[0-9]+\.[0-9]+)\.tar\.(gz|bz2))"''')
+p =
re.compile(r'''href="(/download/0/.*?broad.*?v([0-9]+\.[0-9]+\.[0-9]+)\.tar\.(gz|bz2))"''')
versions = {}
with open(tmp_file) as f:
@@ -183,7 +183,7 @@ class RefGenesGetter:
print('You can use them with ARIBA like this:')
print('ariba prepareref -f', final_fasta, '-m', final_tsv,
'output_directory\n')
print('If you use this downloaded data, please cite:')
-print('"The Comprehensive Antibiotic Resistance Database", McArthur et
al 2013, PMID: 23650175')
+print('"CARD 2020: antibiotic resistome surveillance with the
comprehensive antibiotic resistance database", Alcock et al 2020, PMID:
31665441')
print('and in your methods say that version', self.version, 'of the
database was used')
@@ -659,6 +659,6 @@ class RefGenesGetter:
print('ariba prepareref -f', final_fasta, '-m',
final_tsv, 'output_directory\n')
else:
-print(f"Nothing to do. Exiting.")
+print(f"Nothing to do. Exiting.")
def run(self, outprefix):
exec('self._get_from_' + self.ref_db + '(outprefix)')
=
setup.py
=
@@ -55,7 +55,7 @@ vcfcall_mod = Extension(
setup(
ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
name='ariba',
-version='2.14.5',
+version='2.14.6',
description='ARIBA: Antibiotic Resistance Identification By Assembly',
packages = find_packages(),
package_data={'ariba': ['test_run_data/*', 'tb_data/*']},
View it on GitLab:
https://salsa.debian.org/med-team/ariba/-/commit/65895acfce631d41922b309c9220fccd8ffdd73a
--
View it on GitLab:
https://salsa.debian.org/med-team/ariba/-/commit/65895acfce631d41922b309c9220fccd8ffdd73a
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[med-svn] [Git][med-team/rna-star][master] fix autopkgtest
Sascha Steinbiss pushed to branch master at Debian Med / rna-star Commits: c3089f70 by Sascha Steinbiss at 2020-09-15T16:31:40+02:00 fix autopkgtest - - - - - 2 changed files: - debian/changelog - debian/tests/control Changes: = debian/changelog = @@ -1,3 +1,9 @@ +rna-star (2.7.5c+dfsg-2) unstable; urgency=medium + + * Fix autopkgtest by allowing output to stderr. + + -- Sascha Steinbiss Tue, 15 Sep 2020 15:45:46 +0200 + rna-star (2.7.5c+dfsg-1) unstable; urgency=medium * New upstream version = debian/tests/control = @@ -1,3 +1,4 @@ Test-Command: debian/tests/run_test.sh STAR Depends: @ +Restrictions: allow-stderr View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/commit/c3089f7065862923e3018598f3158df7bfdfc74e -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/commit/c3089f7065862923e3018598f3158df7bfdfc74e You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/rna-star] Pushed new tag debian/2.7.5c+dfsg-2
Sascha Steinbiss pushed new tag debian/2.7.5c+dfsg-2 at Debian Med / rna-star -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/tree/debian/2.7.5c+dfsg-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/rna-star] Pushed new tag debian/2.7.5c+dfsg-3
Sascha Steinbiss pushed new tag debian/2.7.5c+dfsg-3 at Debian Med / rna-star -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/tree/debian/2.7.5c+dfsg-3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/rna-star][master] source upload to enable testing migration
Sascha Steinbiss pushed to branch master at Debian Med / rna-star Commits: 49decd86 by Sascha Steinbiss at 2020-09-16T09:02:08+02:00 source upload to enable testing migration - - - - - 1 changed file: - debian/changelog Changes: = debian/changelog = @@ -1,3 +1,11 @@ +rna-star (2.7.5c+dfsg-3) unstable; urgency=medium + + * Source upload to enable testing migration. + * Confirmed autopkgtest fixed. +Closes: #970340 + + -- Sascha Steinbiss Wed, 16 Sep 2020 08:56:26 +0200 + rna-star (2.7.5c+dfsg-2) unstable; urgency=medium * Fix autopkgtest by allowing output to stderr. View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/commit/49decd86393295876a3eb9d337e0107e6b76279f -- View it on GitLab: https://salsa.debian.org/med-team/rna-star/-/commit/49decd86393295876a3eb9d337e0107e6b76279f You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/augustus] Pushed new tag debian/3.3.3+dfsg-4
Sascha Steinbiss pushed new tag debian/3.3.3+dfsg-4 at Debian Med / augustus -- View it on GitLab: https://salsa.debian.org/med-team/augustus/-/tree/debian/3.3.3+dfsg-4 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/augustus][pristine-tar] pristine-tar data for augustus_3.4.0+dfsg2.orig.tar.xz
Sascha Steinbiss pushed to branch pristine-tar at Debian Med / augustus Commits: 79a32f63 by Sascha Steinbiss at 2020-12-29T00:13:18+01:00 pristine-tar data for augustus_3.4.0+dfsg2.orig.tar.xz - - - - - 2 changed files: - + augustus_3.4.0+dfsg2.orig.tar.xz.delta - + augustus_3.4.0+dfsg2.orig.tar.xz.id Changes: = augustus_3.4.0+dfsg2.orig.tar.xz.delta = Binary files /dev/null and b/augustus_3.4.0+dfsg2.orig.tar.xz.delta differ = augustus_3.4.0+dfsg2.orig.tar.xz.id = @@ -0,0 +1 @@ +ce2c265a7d0d9d085de1e07d7cad5d1fdd548abc View it on GitLab: https://salsa.debian.org/med-team/augustus/-/commit/79a32f63adf190df2126fee7ec5cd70cf2147fd3 -- View it on GitLab: https://salsa.debian.org/med-team/augustus/-/commit/79a32f63adf190df2126fee7ec5cd70cf2147fd3 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/augustus][master] 14 commits: remove docs tutorial dir from Files-Excluded
Sascha Steinbiss pushed to branch master at Debian Med / augustus Commits: 7d19785a by Sascha Steinbiss at 2020-12-28T18:38:02+01:00 remove docs tutorial dir from Files-Excluded - - - - - da55a5ec by Sascha Steinbiss at 2020-12-28T23:56:43+01:00 extend doc-base - - - - - 49d81656 by Sascha Steinbiss at 2020-12-28T23:57:16+01:00 update d/changelog - - - - - 5938fa3d by Sascha Steinbiss at 2020-12-28T23:57:57+01:00 use patches prepared by upstream - - - - - f66f74bc by Sascha Steinbiss at 2020-12-28T23:58:19+01:00 remove obsolete directories from Files-Excluded - - - - - ebbe9d50 by Sascha Steinbiss at 2020-12-28T23:58:43+01:00 add Suggests for dependencies of the scripts - - - - - 9f22f818 by Sascha Steinbiss at 2020-12-28T23:59:10+01:00 add some new build-deps and remove old libbam-dev build-dep - - - - - 5a5596cb by Sascha Steinbiss at 2020-12-28T23:59:54+01:00 remove Build-Using mechanics for libbam-dev - - - - - 1ae0f94a by Sascha Steinbiss at 2020-12-29T00:00:07+01:00 add some additional tools to install - - - - - bf78fa38 by Sascha Steinbiss at 2020-12-29T00:00:27+01:00 New upstream version 3.4.0+dfsg2 - - - - - a8b7df07 by Sascha Steinbiss at 2020-12-29T00:13:18+01:00 Update upstream source from tag 'upstream/3.4.0+dfsg2' Update to upstream version '3.4.0+dfsg2' with Debian dir 7c88fbdda665e4a0ef38baac502a044608b8bb7a - - - - - 9e819963 by Sascha Steinbiss at 2020-12-29T01:10:40+01:00 final 3.4.0 cleanups - - - - - c0986aff by Sascha Steinbiss at 2020-12-29T01:15:51+01:00 adjust doc-base - - - - - 7074dce9 by Sascha Steinbiss at 2020-12-29T01:16:23+01:00 remove obsolete "Team upload" changelog entry - - - - - 30 changed files: - debian/augustus-doc.doc-base - debian/changelog - debian/control - debian/copyright - − debian/patches/buildflags.patch - debian/patches/interpreter_paths.patch - debian/patches/keep_cflags - debian/patches/search_config_path - debian/patches/series - debian/patches/set_installdir - + debian/patches/switch_cgp_testing_off.patch - debian/rules - + docs/tutorial2015/augustus.css - + docs/tutorial2015/data/chr2L.sm.fa.gz - + docs/tutorial2015/data/rnaseq1.fq - + docs/tutorial2015/data/rnaseq2.fq - + docs/tutorial2015/index.html - + docs/tutorial2015/ittrain.html - + docs/tutorial2015/ppx.html - + docs/tutorial2015/prediction.html - + docs/tutorial2015/results/README.TXT - + docs/tutorial2015/results/aug.nasonia.1-1M.gff - + docs/tutorial2015/results/aug.nasonia.hints.gff - + docs/tutorial2015/results/aug.tomato.1-1M.gff - + docs/tutorial2015/results/aug.zebrafish.1-1M.gff - + docs/tutorial2015/results/chrom.sizes - + docs/tutorial2015/results/customtrack - + docs/tutorial2015/results/customtrack.whints.gz - + docs/tutorial2015/results/do.sh - + docs/tutorial2015/results/firsttest.out The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/augustus/-/compare/f6b3fb3b199d4dd23b41246b6b5b62ff739d9acd...7074dce9b495056524a197459dd1b6a0a9f8edf2 -- View it on GitLab: https://salsa.debian.org/med-team/augustus/-/compare/f6b3fb3b199d4dd23b41246b6b5b62ff739d9acd...7074dce9b495056524a197459dd1b6a0a9f8edf2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/augustus][upstream] New upstream version 3.4.0+dfsg2
Sascha Steinbiss pushed to branch upstream at Debian Med / augustus Commits: bf78fa38 by Sascha Steinbiss at 2020-12-29T00:00:27+01:00 New upstream version 3.4.0+dfsg2 - - - - - 30 changed files: - + docs/tutorial2015/augustus.css - + docs/tutorial2015/data/chr2L.sm.fa.gz - + docs/tutorial2015/data/rnaseq1.fq - + docs/tutorial2015/data/rnaseq2.fq - + docs/tutorial2015/index.html - + docs/tutorial2015/ittrain.html - + docs/tutorial2015/ppx.html - + docs/tutorial2015/prediction.html - + docs/tutorial2015/results/README.TXT - + docs/tutorial2015/results/aug.nasonia.1-1M.gff - + docs/tutorial2015/results/aug.nasonia.hints.gff - + docs/tutorial2015/results/aug.tomato.1-1M.gff - + docs/tutorial2015/results/aug.zebrafish.1-1M.gff - + docs/tutorial2015/results/chrom.sizes - + docs/tutorial2015/results/customtrack - + docs/tutorial2015/results/customtrack.whints.gz - + docs/tutorial2015/results/do.sh - + docs/tutorial2015/results/firsttest.out - + docs/tutorial2015/results/genes.gb - + docs/tutorial2015/results/genes.gb.test - + docs/tutorial2015/results/genes.gb.train - + docs/tutorial2015/results/hints.gff - + docs/tutorial2015/results/hints.intron.gff - + docs/tutorial2015/results/rnaseq.bam - + docs/tutorial2015/results/rnaseq.bam.bai - + docs/tutorial2015/results/rnaseq.bw - + docs/tutorial2015/results/rnaseq.wig - + docs/tutorial2015/results/supported.lst - + docs/tutorial2015/scipio.html - + docs/tutorial2015/training.html The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/augustus/-/commit/bf78fa38ef805efc8b1e3bc3a5ab38ee04e0bab8 -- View it on GitLab: https://salsa.debian.org/med-team/augustus/-/commit/bf78fa38ef805efc8b1e3bc3a5ab38ee04e0bab8 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/augustus] Pushed new tag debian/3.4.0+dfsg2-1
Sascha Steinbiss pushed new tag debian/3.4.0+dfsg2-1 at Debian Med / augustus -- View it on GitLab: https://salsa.debian.org/med-team/augustus/-/tree/debian/3.4.0+dfsg2-1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/augustus] Pushed new tag upstream/3.4.0+dfsg2
Sascha Steinbiss pushed new tag upstream/3.4.0+dfsg2 at Debian Med / augustus -- View it on GitLab: https://salsa.debian.org/med-team/augustus/-/tree/upstream/3.4.0+dfsg2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/augustus][master] adjust dversionmangle
Sascha Steinbiss pushed to branch master at Debian Med / augustus Commits: 501c80a8 by Sascha Steinbiss at 2020-12-29T01:46:11+01:00 adjust dversionmangle - - - - - 2 changed files: - debian/changelog - debian/watch Changes: = debian/changelog = @@ -1,3 +1,9 @@ +augustus (3.4.0+dfsg2-2) UNRELEASED; urgency=medium + + * Fix dversionmangle to allow for +dfsgX suffixes. + + -- Sascha Steinbiss Tue, 29 Dec 2020 01:45:47 +0100 + augustus (3.4.0+dfsg2-1) unstable; urgency=medium [ Steffen Moeller ] = debian/watch = @@ -1,4 +1,4 @@ version=4 -opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \ +opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg[0-9]?//g,repack,compression=xz" \ https://github.com/Gaius-Augustus/Augustus/releases .*/archive/v?(\d[.\d]+)[-tag0-9]*@ARCHIVE_EXT@ View it on GitLab: https://salsa.debian.org/med-team/augustus/-/commit/501c80a8fe995c727f37b85fc0bae9bbab924d5f -- View it on GitLab: https://salsa.debian.org/med-team/augustus/-/commit/501c80a8fe995c727f37b85fc0bae9bbab924d5f You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/augustus][master] 2 commits: run tests without --compare
Sascha Steinbiss pushed to branch master at Debian Med / augustus
Commits:
5496e119 by Sascha Steinbiss at 2021-01-03T16:23:29+01:00
run tests without --compare
- - - - -
21352fdf by Sascha Steinbiss at 2021-01-03T16:36:15+01:00
update d/changelog
- - - - -
3 changed files:
- debian/changelog
- + debian/patches/disable-compare.patch
- debian/patches/series
Changes:
=
debian/changelog
=
@@ -1,8 +1,10 @@
-augustus (3.4.0+dfsg2-2) UNRELEASED; urgency=medium
+augustus (3.4.0+dfsg2-2) unstable; urgency=medium
* Fix dversionmangle to allow for +dfsgX suffixes.
+ * Run tests without --compare. This hopefully fixes FTBFS due to different
+results on different platforms, not matching the reference.
- -- Sascha Steinbiss Tue, 29 Dec 2020 01:45:47 +0100
+ -- Sascha Steinbiss Sun, 03 Jan 2021 16:10:48 +0100
augustus (3.4.0+dfsg2-1) unstable; urgency=medium
=
debian/patches/disable-compare.patch
=
@@ -0,0 +1,13 @@
+--- a/Makefile
b/Makefile
+@@ -42,8 +42,8 @@
+ cd ..; tar -czf augustus-$(AUGVERSION).tar.gz augustus-$(AUGVERSION)
+
+ test:
+- cd tests/examples && ./testcases.py --compare --html
+- tests/auxprogs/bam2wig/test_bam2wig.py --compare --html
++ cd tests/examples && ./testcases.py --html
++ tests/auxprogs/bam2wig/test_bam2wig.py --html
+
+ unit_test:
+ cd src && ${MAKE} unittest
=
debian/patches/series
=
@@ -2,3 +2,4 @@ search_config_path
set_installdir
interpreter_paths.patch
switch_cgp_testing_off.patch
+disable-compare.patch
View it on GitLab:
https://salsa.debian.org/med-team/augustus/-/compare/501c80a8fe995c727f37b85fc0bae9bbab924d5f...21352fdf25a6616c43f53d1a3b68eb007adca965
--
View it on GitLab:
https://salsa.debian.org/med-team/augustus/-/compare/501c80a8fe995c727f37b85fc0bae9bbab924d5f...21352fdf25a6616c43f53d1a3b68eb007adca965
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[med-svn] [Git][med-team/augustus] Pushed new tag debian/3.4.0+dfsg2-2
Sascha Steinbiss pushed new tag debian/3.4.0+dfsg2-2 at Debian Med / augustus -- View it on GitLab: https://salsa.debian.org/med-team/augustus/-/tree/debian/3.4.0+dfsg2-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/gffread] Pushed new tag debian/0.12.1-4
Sascha Steinbiss pushed new tag debian/0.12.1-4 at Debian Med / gffread -- View it on GitLab: https://salsa.debian.org/med-team/gffread/-/tree/debian/0.12.1-4 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/gffread][master] skip broken new AUGUSTUS examples in autopkgtest
Sascha Steinbiss pushed to branch master at Debian Med / gffread
Commits:
393dcda1 by Sascha Steinbiss at 2021-01-08T09:04:39+01:00
skip broken new AUGUSTUS examples in autopkgtest
- - - - -
2 changed files:
- debian/changelog
- debian/tests/run-tests
Changes:
=
debian/changelog
=
@@ -1,3 +1,11 @@
+gffread (0.12.1-4) unstable; urgency=medium
+
+ * Team upload.
+ * Skip some new AUGUSTUS GTFs that are likely bad, causing autopkgtests to
+fail.
+
+ -- Sascha Steinbiss Fri, 08 Jan 2021 08:52:52 +0100
+
gffread (0.12.1-3) unstable; urgency=medium
* Team upload
=
debian/tests/run-tests
=
@@ -113,7 +113,7 @@ IFS=", " read -r -a pkgs <<< ${PACKAGES}
# gffread /usr/lib/python3/dist-packages/pybedtools/test/data/c.gff
# Error: discarding overlapping duplicate mRNA feature (496-576) with
ID=AT1G01010.mRNA
-SKIPS="/usr/share/doc/augustus/tutorial/results/augustus.abinitio.gff|/usr/share/doc/augustus/tutorial/results/augustus.hints.gff|/usr/lib/R/site-library/Gviz/extdata/test.gff2|/usr/lib/R/site-library/rtracklayer/tests/genes.gff3|/usr/share/EMBOSS/test/data/featexample2.gff3|/usr/share/EMBOSS/test/data/gmod-quantitative.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_all.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_bacs.gff3|/var/lib/gbrowse/databases/ideograms/human_cytobands.gff|/var/lib/gbrowse/databases/ideograms/mouse_cytobands.gff|/var/lib/gbrowse/databases/ideograms/rat_cytobands.gff|/var/lib/gbrowse/databases/yeast_chr1\+2/yeast_chr1\+2.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/F3-unique-3.v2.gff|/usr/lib/python3/dist-packages/gffutils/test/data/mouse_extra_comma.gff3|/usr/lib/R/site-library/GenomicFeatures/extdata/GFF3_files/TheCanonicalGene_v2.gff3|/usr/share/doc/seqan-apps/insegt/example/annoOutput.gff|/usr/lib/python3/dist-packages/optimir/resources/coordinates/hsa_miRCarta_v1.1.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff|/usr/lib/python3/dist-packages/gffutils/test/data/glimmer_nokeyval.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/unsanitized.gff|/usr/lib/python3/dist-packages/pybedtools/test/data/c.gff|/usr/lib/R/site-library/rtracklayer/tests/v2.gff|/usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.gff|/usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.sim.gff"
+SKIPS="/usr/share/doc/augustus/tutorial-cgp|/usr/share/doc/augustus/tutorial/results/augustus.abinitio.gff|/usr/share/doc/augustus/tutorial/results/augustus.hints.gff|/usr/lib/R/site-library/Gviz/extdata/test.gff2|/usr/lib/R/site-library/rtracklayer/tests/genes.gff3|/usr/share/EMBOSS/test/data/featexample2.gff3|/usr/share/EMBOSS/test/data/gmod-quantitative.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_all.gff3|/usr/share/gbrowse/htdocs/tutorial/data_files/volvox_bacs.gff3|/var/lib/gbrowse/databases/ideograms/human_cytobands.gff|/var/lib/gbrowse/databases/ideograms/mouse_cytobands.gff|/var/lib/gbrowse/databases/ideograms/rat_cytobands.gff|/var/lib/gbrowse/databases/yeast_chr1\+2/yeast_chr1\+2.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/F3-unique-3.v2.gff|/usr/lib/python3/dist-packages/gffutils/test/data/mouse_extra_comma.gff3|/usr/lib/R/site-library/GenomicFeatures/extdata/GFF3_files/TheCanonicalGene_v2.gff3|/usr/share/doc/seqan-apps/insegt/example/annoOutput.gff|/usr/lib/python3/dist-packages/optimir/resources/coordinates/hsa_miRCarta_v1.1.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/dmel-all-no-analysis-r5.49_50k_lines.gff|/usr/lib/python3/dist-packages/gffutils/test/data/glimmer_nokeyval.gff3|/usr/lib/python3/dist-packages/gffutils/test/data/unsanitized.gff|/usr/lib/python3/dist-packages/pybedtools/test/data/c.gff|/usr/lib/R/site-library/rtracklayer/tests/v2.gff|/usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.gff|/usr/share/doc/gff2aplot/examples/mhcregion/hs-mm.sim.gff"
for package in "${pkgs[@]}"
do
View it on GitLab:
https://salsa.debian.org/med-team/gffread/-/commit/393dcda1b32d83199ad144655608aaf038ce6144
--
View it on GitLab:
https://salsa.debian.org/med-team/gffread/-/commit/393dcda1b32d83199ad144655608aaf038ce6144
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[med-svn] [Git][med-team/codonw] Pushed new tag debian/1.4.4-6
Sascha Steinbiss pushed new tag debian/1.4.4-6 at Debian Med / codonw -- View it on GitLab: https://salsa.debian.org/med-team/codonw/-/tree/debian/1.4.4-6 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/nanopolish][master] 2 commits: patch code to not define PR_R7 and PT_R9
Sascha Steinbiss pushed to branch master at Debian Med / nanopolish
Commits:
df0f8daa by Sascha Steinbiss at 2021-02-20T15:48:49+01:00
patch code to not define PR_R7 and PT_R9
- - - - -
0d4caf1e by Sascha Steinbiss at 2021-02-20T15:49:09+01:00
add patch
- - - - -
3 changed files:
- debian/changelog
- + debian/patches/rename_enum.patch
- debian/patches/series
Changes:
=
debian/changelog
=
@@ -1,3 +1,12 @@
+nanopolish (0.13.2-2) unstable; urgency=medium
+
+ * Team upload.
+ * Patch code to not define PR_R7 and PT_R9 to avoid FTBFS on
+some archs (Closes: #960634)
+Thanks to Barry Arndt for the hint.
+
+ -- Sascha Steinbiss Sat, 20 Feb 2021 15:06:55 +0100
+
nanopolish (0.13.2-1) unstable; urgency=medium
[ Michael R. Crusoe ]
=
debian/patches/rename_enum.patch
=
@@ -0,0 +1,109 @@
+Description: do not define PT_R{7,9}
+ Defining these enum values will cause a FTBFS on some architectures
+ due to them already existing in some architecture-dependent headers.
+ We rename them to avoid clashes. Thanks to Barry Arndt fot the hint.
+Author: Sascha Steinbiss
+Forwarded: https://github.com/jts/nanopolish/issues/883
+Last-Update: 2021-02-20
+--- a/src/hmm/nanopolish_profile_hmm.cpp
b/src/hmm/nanopolish_profile_hmm.cpp
+@@ -22,7 +22,7 @@
+
+ float profile_hmm_score(const HMMInputSequence& sequence, const HMMInputData&
data, const uint32_t flags)
+ {
+-if(data.read->pore_type == PT_R9) {
++if(data.read->pore_type == PORETYPE_R9) {
+ return profile_hmm_score_r9(sequence, data, flags);
+ } else {
+ return profile_hmm_score_r7(sequence, data, flags);
+@@ -57,7 +57,7 @@
+
+ std::vector profile_hmm_align(const HMMInputSequence&
sequence, const HMMInputData& data, const uint32_t flags)
+ {
+-if(data.read->pore_type == PT_R9) {
++if(data.read->pore_type == PORETYPE_R9) {
+ return profile_hmm_align_r9(sequence, data, flags);
+ } else {
+ return profile_hmm_align_r7(sequence, data, flags);
+--- a/src/nanopolish_call_variants.cpp
b/src/nanopolish_call_variants.cpp
+@@ -673,7 +673,7 @@
+
+ double num_kmers = variant_offset_end - variant_offset_start;
+ double log_gamma = sum_duration > MIN_DURATION ?
DurationModel::log_gamma_sum(sum_duration, params, num_kmers) : 0.0f;
+-if(read->pore_type == PT_R9) {
++if(read->pore_type == PORETYPE_R9) {
+ duration_likelihoods[var_sequence_length] += log_gamma;
+ }
+ if(opt::verbose > 3) {
+--- a/src/nanopolish_squiggle_read.cpp
b/src/nanopolish_squiggle_read.cpp
+@@ -106,7 +106,7 @@
+ void SquiggleRead::init(const std::string& read_sequence, const Fast5Data&
data, const uint32_t flags)
+ {
+ this->nucleotide_type = SRNT_DNA;
+-this->pore_type = PT_UNKNOWN;
++this->pore_type = PORETYPE_UNKNOWN;
+ this->f_p = nullptr;
+
+ this->events_per_base[0] = events_per_base[1] = 0.0f;
+@@ -219,7 +219,7 @@
+ // in this case, we have to set this strand to be invalid
+ if(!event_maps_1d[si].empty()) {
+ // run version-specific load
+-if(pore_type == PT_R7) {
++if(pore_type == PORETYPE_R7) {
+ _load_R7(si);
+ } else {
+ _load_R9(si, read_sequences_1d[si], event_maps_1d[si],
p_model_states, flags);
+@@ -231,10 +231,10 @@
+
+ // Build the map from k-mers of the read sequence to events
+ if(read_type == SRT_2D) {
+-if(pore_type == PT_R9) {
++if(pore_type == PORETYPE_R9) {
+ build_event_map_2d_r9();
+ } else {
+-assert(pore_type == PT_R7);
++assert(pore_type == PORETYPE_R7);
+ build_event_map_2d_r7();
+ }
+ } else {
+@@ -298,7 +298,7 @@
+ }
+
+ this->read_type = SRT_TEMPLATE;
+-this->pore_type = PT_R9;
++this->pore_type = PORETYPE_R9;
+
+ // Set the base model for this read to either the nucleotide or U->T RNA
model
+ this->base_model[strand_idx] = PoreModelSet::get_model(kit, alphabet,
strand_str, k);
+@@ -1122,11 +1122,11 @@
+ assert(f_p and f_p->is_open());
+ if (f_p->have_basecall_model(0))
+ {
+-pore_type = PT_R7;
++pore_type = PORETYPE_R7;
+ }
+ else
+ {
+-pore_type = PT_R9;
++pore_type = PORETYPE_R9;
+ }
+ }
+
+--- a/src/nanopolish_squiggle_read.h
b/src/nanopolish_squiggle_read.h
+@@ -21,9 +21,9 @@
+
+ enum PoreType
+ {
+-PT_UNKNOWN = 0,
+-PT_R7,
+-PT_R9,
++PORETYPE_UNKNOWN = 0,
++PORETYPE_R7,
++PORETYPE_R9,
+ };
+
+ // the type of the read
=
debian/patches/series
=
[med-svn] [Git][med-team/nanopolish] Pushed new tag debian/0.13.2-2
Sascha Steinbiss pushed new tag debian/0.13.2-2 at Debian Med / nanopolish -- View it on GitLab: https://salsa.debian.org/med-team/nanopolish/-/tree/debian/0.13.2-2 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libace-perl] Pushed new tag debian/1.92-10
Sascha Steinbiss pushed new tag debian/1.92-10 at Debian Med / libace-perl -- View it on GitLab: https://salsa.debian.org/med-team/libace-perl/-/tree/debian/1.92-10 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libace-perl][master] respect hardening flags
Sascha Steinbiss pushed to branch master at Debian Med / libace-perl Commits: 10682690 by Sascha Steinbiss at 2021-02-20T17:22:31+01:00 respect hardening flags - - - - - 3 changed files: - debian/changelog - + debian/patches/hardening.patch - debian/patches/series Changes: = debian/changelog = @@ -1,3 +1,11 @@ +libace-perl (1.92-10) unstable; urgency=medium + + * Team upload. + * Make acelib C Makefile respect hardening CFLAGS and CPPFLAGS. +Closes: #974196 + + -- Sascha Steinbiss Sat, 20 Feb 2021 17:14:04 +0100 + libace-perl (1.92-9) unstable; urgency=medium [ Matthias Klose ] = debian/patches/hardening.patch = @@ -0,0 +1,22 @@ +--- a/acelib/Makefile b/acelib/Makefile +@@ -42,8 +42,8 @@ + ## Different platforms use CC or COMPILE.c + # (USEROPTS - see comments at top of file) + # +-CC =$(COMPILER) $(USEROPTS) $(IDIR) -D$(NAME) -c +-COMPILE.c = $(COMPILER) $(USEROPTS) $(IDIR) -D$(NAME) -c ++CC =$(COMPILER) $(CFLAGS) $(CPPFLAGS) $(USEROPTS) $(IDIR) -D$(NAME) -c ++COMPILE.c = $(COMPILER) $(CFLAGS) $(CPPFLAGS) $(USEROPTS) $(IDIR) -D$(NAME) -c + + ### + ## make targets. +@@ -106,7 +106,7 @@ + rpcace_sp.o: rpcace_sp.c rpcace_svc.c + + aceclientlib.o: aceclientlib.c rpcace.h +- $(CC) -c $< ++ $(CC) $(LDFLAGS) -c $< + + RPC_CLIENT_OBJS = aceclientlib.o rpcace_clnt.o rpcace_xdr.o + RPC_SERVER_OBJS = rpcace_sp.o rpcace_xdr.o = debian/patches/series = @@ -2,3 +2,4 @@ spelling.patch parallel-ftbfs.patch defined_hash_array.patch libtirpc.patch +hardening.patch View it on GitLab: https://salsa.debian.org/med-team/libace-perl/-/commit/106826902ca49dc418f2cc8d7c5fbf6f05603967 -- View it on GitLab: https://salsa.debian.org/med-team/libace-perl/-/commit/106826902ca49dc418f2cc8d7c5fbf6f05603967 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libssw][master] 3 commits: do not hardcode source/target version levels
Sascha Steinbiss pushed to branch master at Debian Med / libssw Commits: 687032ec by Sascha Steinbiss at 2021-02-20T21:51:04+01:00 do not hardcode source/target version levels - - - - - 6ce25676 by Sascha Steinbiss at 2021-02-20T21:51:12+01:00 bump Standards-Version - - - - - 77459033 by Sascha Steinbiss at 2021-02-20T21:51:20+01:00 use watchfile version 4 - - - - - 5 changed files: - debian/changelog - debian/control - debian/patches/build_all_libs.patch - debian/patches/hardening.patch - debian/watch Changes: = debian/changelog = @@ -1,3 +1,12 @@ +libssw (1.1-13) unstable; urgency=medium + + * Do not hardcode source/target version levels into javac call. +Closes: #982045 + * Bump Standards-Version. + * Use watchfile version 4. + + -- Sascha Steinbiss Sat, 20 Feb 2021 21:21:08 +0100 + libssw (1.1-12) unstable; urgency=medium * Mark one symbol as optional, disappearing on s390x with -O3 = debian/control = @@ -12,7 +12,7 @@ Build-Depends: debhelper (>= 12~), zlib1g-dev, libsimde-dev, maven-repo-helper -Standards-Version: 4.5.0 +Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/libssw Vcs-Git: https://salsa.debian.org/med-team/libssw.git Homepage: https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library = debian/patches/build_all_libs.patch = @@ -6,7 +6,7 @@ Description: build all libraries Author: Sascha Steinbiss --- a/src/Makefile +++ b/src/Makefile -@@ -5,26 +5,31 @@ CXXFLAGS := $(CFLAGS) +@@ -5,26 +5,31 @@ LOBJS = ssw.o LCPPOBJS = ssw_cpp.o PROG = ssw_test @@ -45,7 +45,7 @@ Author: Sascha Steinbiss $(EXAMPLE): example.c -@@ -38,10 +43,10 @@ $(JAVA_LIB): sswjni.c ssw.c ssw.h +@@ -38,10 +43,10 @@ $(CC) $(CFLAGS) $(JAVA_INLCUDES) -fPIC -shared -rdynamic -o $@ $< ssw.c $(JAVA_JAR): $(JAVA_OBJ) @@ -54,11 +54,11 @@ Author: Sascha Steinbiss %.class: %.java - javac -cp ./ $< -+ javac -target 1.6 -source 1.6 $< ++ javac $< ssw.o: ssw.c ssw.h $(CC) -c -o $@ $< $(CFLAGS) -@@ -50,4 +55,4 @@ ssw_cpp.o: ssw_cpp.cpp ssw_cpp.h ssw.h +@@ -50,4 +55,4 @@ $(CXX) -c -o $@ $< $(CXXFLAGS) clean: = debian/patches/hardening.patch = @@ -15,7 +15,7 @@ Author: Sascha Steinbiss LOBJS = ssw.o LCPPOBJS = ssw_cpp.o PROG = ssw_test -@@ -24,7 +25,7 @@ all: default java +@@ -24,7 +25,7 @@ java: $(JAVA_JAR) $(JAVA_LIB) $(LIB): ssw.c ssw.h ssw_cpp.h ssw_cpp.cpp @@ -24,7 +24,7 @@ Author: Sascha Steinbiss $(STATICLIB): $(LOBJS) $(LCPPOBJS) ar rcs $@ $^ -@@ -34,13 +35,13 @@ $(PROG): main.c kseq.h +@@ -34,13 +35,13 @@ $(EXAMPLE): example.c $(PROG) $(EXAMPLE): $(LOBJS) @@ -41,8 +41,8 @@ Author: Sascha Steinbiss $(JAVA_JAR): $(JAVA_OBJ) jar cvf $@ $^ -@@ -49,10 +50,10 @@ $(JAVA_JAR): $(JAVA_OBJ) - javac -target 1.6 -source 1.6 $< +@@ -49,10 +50,10 @@ + javac $< ssw.o: ssw.c ssw.h - $(CC) -c -o $@ $< $(CFLAGS) = debian/watch = @@ -1,2 +1,2 @@ -version=3 +version=4 https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/tags .*/v?(\d.*)\.(?:tgz|tbz2|txz|tar\.(?:gz|bz2|xz)) View it on GitLab: https://salsa.debian.org/med-team/libssw/-/compare/09413a4a3c713949b6e9d9e05f636561df9293b9...77459033989459e978a00a5fb60415289241f3fd -- View it on GitLab: https://salsa.debian.org/med-team/libssw/-/compare/09413a4a3c713949b6e9d9e05f636561df9293b9...77459033989459e978a00a5fb60415289241f3fd You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/libssw] Pushed new tag debian/1.1-13
Sascha Steinbiss pushed new tag debian/1.1-13 at Debian Med / libssw -- View it on GitLab: https://salsa.debian.org/med-team/libssw/-/tree/debian/1.1-13 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/jellyfish][master] silence warning gone error with -O3
Sascha Steinbiss pushed to branch master at Debian Med / jellyfish
Commits:
b3ca453b by Sascha Steinbiss at 2021-02-21T12:10:39+01:00
silence warning gone error with -O3
I could not reproduce this with only upstream code, and with -O2 the
code builds fine, so I do not assume this is a coding error but an
optimization quirk. Disabling this particular compiler warning since
tests also finish fine.
- - - - -
2 changed files:
- debian/changelog
- debian/rules
Changes:
=
debian/changelog
=
@@ -1,3 +1,11 @@
+jellyfish (2.3.0-8.1) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Silence additional warning/error appearing with -O3.
+Closes: #973431
+
+ -- Sascha Steinbiss Sun, 21 Feb 2021 12:09:45 +0100
+
jellyfish (2.3.0-8) unstable; urgency=medium
* Add Breaks+Replaces: jellyfish-examples (<< 2.3.0-7)
=
debian/rules
=
@@ -15,6 +15,7 @@ export PERL_MM_OPT=INSTALLDIRS=vendor
export PYBUILD_BUILD_ARGS=build_ext -L${CURDIR}/.libs
export DEB_LDFLAGS_MAINT_APPEND = -lpthread
+export DEB_CXXFLAGS_MAINT_APPEND = -Wno-nonnull
export PYBUILD_NAME = dna_jellyfish
%:
View it on GitLab:
https://salsa.debian.org/med-team/jellyfish/-/commit/b3ca453ba701a4bedf168d84e865ccd33d81b697
--
View it on GitLab:
https://salsa.debian.org/med-team/jellyfish/-/commit/b3ca453ba701a4bedf168d84e865ccd33d81b697
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[med-svn] [Git][med-team/jellyfish][master] restrict archs
Sascha Steinbiss pushed to branch master at Debian Med / jellyfish
Commits:
363126f1 by Sascha Steinbiss at 2021-02-21T18:02:24+01:00
restrict archs
- - - - -
2 changed files:
- debian/changelog
- debian/control
Changes:
=
debian/changelog
=
@@ -1,8 +1,11 @@
-jellyfish (2.3.0-8.1) UNRELEASED; urgency=medium
+jellyfish (2.3.0-9) unstable; urgency=medium
* Team upload.
* Silence additional warning/error appearing with -O3.
Closes: #973431
+ * Restrict to architectures that support the atomic instructions used by
+upstream.
+Closes: #976340
-- Sascha Steinbiss Sun, 21 Feb 2021 12:09:45 +0100
=
debian/control
=
@@ -27,7 +27,7 @@ Homepage: https://www.cbcb.umd.edu/software/jellyfish/
Rules-Requires-Root: no
Package: jellyfish
-Architecture: any
+Architecture: amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386
ia64 kfreebsd-amd64 kfreebsd-i386 riscv64
Depends: ${shlibs:Depends},
${misc:Depends},
libjellyfish-2.0-2 (= ${binary:Version})
@@ -49,7 +49,7 @@ Description: count k-mers in DNA sequences
format using the "jellyfish dump" command.
Package: libjellyfish-2.0-2
-Architecture: any
+Architecture: amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386
ia64 kfreebsd-amd64 kfreebsd-i386 riscv64
Multi-Arch: same
Section: libs
Depends: ${shlibs:Depends},
@@ -73,7 +73,7 @@ Description: count k-mers in DNA sequences (dynamic library
of jellyfish)
jellyfish is linked to.
Package: libjellyfish-2.0-dev
-Architecture: any
+Architecture: amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386
ia64 kfreebsd-amd64 kfreebsd-i386 riscv64
Multi-Arch: same
Section: libdevel
Depends: ${misc:Depends},
@@ -97,7 +97,7 @@ Description: count k-mers in DNA sequences (development files
of jellyfish)
header files)
Package: python3-dna-jellyfish
-Architecture: any
+Architecture: amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386
ia64 kfreebsd-amd64 kfreebsd-i386 riscv64
Section: python
Depends: ${python3:Depends},
${misc:Depends},
@@ -120,7 +120,7 @@ Description: count k-mers in DNA sequences (Python bindings
of jellyfish)
This package contains the Python bindings of jellyfish.
Package: libjellyfish-perl
-Architecture: any
+Architecture: amd64 arm64 armel armhf i386 mips64el ppc64el hppa hurd-i386
ia64 kfreebsd-amd64 kfreebsd-i386 riscv64
Multi-Arch: same
Section: perl
Depends: ${perl:Depends},
View it on GitLab:
https://salsa.debian.org/med-team/jellyfish/-/commit/363126f1f6d955fd58061577cb7073d03eafc6e1
--
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[med-svn] [Git][med-team/jellyfish] Pushed new tag debian/2.3.0-9
Sascha Steinbiss pushed new tag debian/2.3.0-9 at Debian Med / jellyfish -- View it on GitLab: https://salsa.debian.org/med-team/jellyfish/-/tree/debian/2.3.0-9 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools] Pushed new branch experimental
Sascha Steinbiss pushed new branch experimental at Debian Med / genometools -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/tree/experimental You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [Git][med-team/genometools] Pushed new tag debian/1.6.1+ds-5_exp1
Sascha Steinbiss pushed new tag debian/1.6.1+ds-5_exp1 at Debian Med / genometools -- View it on GitLab: https://salsa.debian.org/med-team/genometools/-/tree/debian/1.6.1+ds-5_exp1 You're receiving this email because of your account on salsa.debian.org. ___ debian-med-commit mailing list debian-med-com...@alioth-lists.debian.net https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11598 - trunk/packages
Author: sascha-guest Date: 2012-07-06 14:52:13 + (Fri, 06 Jul 2012) New Revision: 11598 Added: trunk/packages/genometools/ Log: create GenomeTools package directory ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11599 - in trunk/packages/genometools: . trunk trunk/debian trunk/debian/patches trunk/debian/source
Author: sascha-guest
Date: 2012-07-06 14:54:49 + (Fri, 06 Jul 2012)
New Revision: 11599
Added:
trunk/packages/genometools/trunk/
trunk/packages/genometools/trunk/debian/
trunk/packages/genometools/trunk/debian/changelog
trunk/packages/genometools/trunk/debian/compat
trunk/packages/genometools/trunk/debian/control
trunk/packages/genometools/trunk/debian/copyright
trunk/packages/genometools/trunk/debian/genometools-common.install
trunk/packages/genometools/trunk/debian/genometools-doc.docs
trunk/packages/genometools/trunk/debian/genometools.docs
trunk/packages/genometools/trunk/debian/genometools.install
trunk/packages/genometools/trunk/debian/libgenometools0-dev.install
trunk/packages/genometools/trunk/debian/libgenometools0.install
trunk/packages/genometools/trunk/debian/libgenometools0.links
trunk/packages/genometools/trunk/debian/libgenometools0.postinst
trunk/packages/genometools/trunk/debian/libgenometools0.postrm
trunk/packages/genometools/trunk/debian/patches/
trunk/packages/genometools/trunk/debian/patches/adding_soname
trunk/packages/genometools/trunk/debian/patches/adding_soname.patch
trunk/packages/genometools/trunk/debian/patches/series
trunk/packages/genometools/trunk/debian/rules
trunk/packages/genometools/trunk/debian/source/
trunk/packages/genometools/trunk/debian/source/format
trunk/packages/genometools/trunk/debian/watch
Log:
initial upload of GenomeTools as started at Debian Med Sprint
Property changes on: trunk/packages/genometools/trunk/debian
___
Added: mergeWithUpstream
+ 1
Added: trunk/packages/genometools/trunk/debian/changelog
===
--- trunk/packages/genometools/trunk/debian/changelog
(rev 0)
+++ trunk/packages/genometools/trunk/debian/changelog 2012-07-06 14:54:49 UTC
(rev 11599)
@@ -0,0 +1,5 @@
+genometools (1.4.0-1) unstable; urgency=low
+
+ * Initial release (Closes: #657923)
+
+ -- Sascha Steinbiss Fri, 27 Jan 2012 18:51:44
+0100
Added: trunk/packages/genometools/trunk/debian/compat
===
--- trunk/packages/genometools/trunk/debian/compat
(rev 0)
+++ trunk/packages/genometools/trunk/debian/compat 2012-07-06 14:54:49 UTC
(rev 11599)
@@ -0,0 +1 @@
+7
Added: trunk/packages/genometools/trunk/debian/control
===
--- trunk/packages/genometools/trunk/debian/control
(rev 0)
+++ trunk/packages/genometools/trunk/debian/control 2012-07-06 14:54:49 UTC
(rev 11599)
@@ -0,0 +1,64 @@
+Source: genometools
+Section: science
+Priority: extra
+Maintainer: Sascha Steinbiss
+Build-Depends: debhelper (>= 7.0.50~), quilt, liblua5.1-0-dev,
liblua5.1-lpeg-dev, liblua5.1-md5-dev, liblua5.1-filesystem-dev, libcairo2-dev,
zlib1g-dev, libbz2-dev, libexpat1-dev, libpth-dev, libncurses5-dev
+Standards-Version: 3.9.3
+Homepage: http://genometools.org
+Vcs-Browser:
http://svn.debian.org/viewvc/debian-med/trunk/packages/genometools/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/genometools/trunk/
+
+Package: genometools
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, genometools-common
+Description: versatile genome analysis toolkit
+ The GenomeTools contains a collection of useful tools for bioinformatics,
+ combined into a single binary.
+ .
+ The toolkit contains binaries for sequence and annotation handling,
+ index structure generation and access, efficient matching, annotation
+ visualization and much more.
+
+Package: genometools-common
+Architecture: all
+Depends: ${misc:Depends}, libbam-dev, liblua5.1-md5-0, liblua5.1-0,
liblua5.1-lpeg2, liblua5.1-filesystem0, libcairo2, zlib1g, libbz2-1.0,
libexpat1, libpth20, libncurses5
+Description: shared data files for GenomeTools
+ This package contains configuration files such as
+ alphabet transformations, style files, etc. required to use the
+ GenomeTools executable and/or library.
+
+Package: libgenometools0
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, genometools-common
+Description: versatile genome analysis library
+ This package contains the GenomeTools shared library and header
+ files. It offers efficient sequence analysis components, available
+ via an object-oriented interface, and a collection of useful tools for
+ bioinformatics, combined into a single binary.
+ .
+ The library contains components for sequence and annotation handling,
+ index structure generation and access, efficient matching, annotation
+ visualization and much more.
+
+Package: libgenometools0-dev
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, libgenometools0 (=
${binary:Version})
+Section: libdevel
+Description: development files for GenomeTools
+ This pack
[med-svn] r11648 - in trunk/packages/genometools/trunk/debian: . patches
Author: sascha-guest
Date: 2012-07-09 11:40:22 + (Mon, 09 Jul 2012)
New Revision: 11648
Added:
trunk/packages/genometools/trunk/debian/patches/libbam-fix
Modified:
trunk/packages/genometools/trunk/debian/control
trunk/packages/genometools/trunk/debian/patches/series
trunk/packages/genometools/trunk/debian/rules
Log:
fix GenomeTools package
Modified: trunk/packages/genometools/trunk/debian/control
===
--- trunk/packages/genometools/trunk/debian/control 2012-07-09 11:14:19 UTC
(rev 11647)
+++ trunk/packages/genometools/trunk/debian/control 2012-07-09 11:40:22 UTC
(rev 11648)
@@ -2,7 +2,9 @@
Section: science
Priority: extra
Maintainer: Sascha Steinbiss
-Build-Depends: debhelper (>= 7.0.50~), quilt, liblua5.1-0-dev,
liblua5.1-lpeg-dev, liblua5.1-md5-dev, liblua5.1-filesystem-dev, libcairo2-dev,
zlib1g-dev, libbz2-dev, libexpat1-dev, libpth-dev, libncurses5-dev
+Build-Depends: debhelper (>= 7.0.50~), quilt,
+ liblua5.1-0-dev, liblua5.1-md5-dev, liblua5.1-filesystem-dev,
liblua5.1-lpeg-dev,
+ libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, libncurses5-dev,
libsqlite3-dev, libbam-dev
Standards-Version: 3.9.3
Homepage: http://genometools.org
Vcs-Browser:
http://svn.debian.org/viewvc/debian-med/trunk/packages/genometools/trunk/
@@ -21,7 +23,7 @@
Package: genometools-common
Architecture: all
-Depends: ${misc:Depends}, libbam-dev, liblua5.1-md5-0, liblua5.1-0,
liblua5.1-lpeg2, liblua5.1-filesystem0, libcairo2, zlib1g, libbz2-1.0,
libexpat1, libpth20, libncurses5
+Depends: ${misc:Depends}, liblua5.1-md5-0|liblua5.1-0,
liblua5.1-lpeg2|liblua5.1-0, liblua5.1-filesystem0|liblua5.1-0, liblua5.1-0,
libcairo2, zlib1g, libbz2-1.0, libexpat1, libpth20, libncurses5, libsqlite3-0
Description: shared data files for GenomeTools
This package contains configuration files such as
alphabet transformations, style files, etc. required to use the
Added: trunk/packages/genometools/trunk/debian/patches/libbam-fix
===
--- trunk/packages/genometools/trunk/debian/patches/libbam-fix
(rev 0)
+++ trunk/packages/genometools/trunk/debian/patches/libbam-fix 2012-07-09
11:40:22 UTC (rev 11648)
@@ -0,0 +1,111 @@
+--- genometools-1.4.0.orig/Makefile
genometools-1.4.0/Makefile
+@@ -235,7 +235,7 @@
+ # add necessary shared lib dependencies then not building them ourselves
+ ifeq ($(useshared),yes)
+ DEPLIBS:=-lm -lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \
+- -llua5.1-filesystem -llua5.1-des56 -lbam
++ -llua5.1-filesystem -llua5.1-des56
+ EXP_LDLIBS += $(DEPLIBS)
+ GTSHAREDLIB_LIBDEP += $(DEPLIBS)
+ endif
+@@ -555,6 +555,10 @@
+ @$(RANLIB) $@
+ endif
+
++ifeq ($(useshared),yes)
++ ADDITIONAL_STATIC_DEPS:=/usr/lib/libbam.a
++endif
++
+ lib/libgenometools.a: obj/gt_config.h $(LIBGENOMETOOLS_OBJ)
+ @echo "[link $(@F)]"
+ @test -d $(@D) || mkdir -p $(@D)
+@@ -563,19 +567,13 @@
+ @$(RANLIB) $@
+ endif
+
+-ifneq ($(useshared),yes)
+- ADDITIONAL_SO_DEPS:=lib/libbz2.a \
+- lib/libexpat.a \
+- lib/libz.a
+-endif
+-
+ lib/libgenometools$(SHARED_OBJ_NAME_EXT): obj/gt_config.h \
+ $(LIBGENOMETOOLS_OBJ) \
+- $(ADDITIONAL_SO_DEPS)
++ $(ADDITIONAL_STATIC_DEPS)
+ @echo "[link $(@F)]"
+ @test -d $(@D) || mkdir -p $(@D)
+ @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(SHARED) -Wl,-soname,$(notdir $@)
$(LIBGENOMETOOLS_OBJ) \
+- -o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP)
++ -o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP) $(ADDITIONAL_STATIC_DEPS)
+
+ lib/libtecla.a: $(LIBTECLA_OBJ)
+ @echo "[link $(@F)]"
+@@ -603,48 +601,62 @@
+
+ $(eval $(call PROGRAM_template, bin/skproto, $(SKPROTO_OBJ) \
+ lib/libgenometools.a\
++ $(ADDITIONAL_STATIC_DEPS) \
+ $(OVERRIDELIBS)))
+
+ $(eval $(call PROGRAM_template, bin/gt, $(GTMAIN_OBJ) $(TOOLS_OBJ) \
+ lib/libgenometools.a \
++$(ADDITIONAL_STATIC_DEPS) \
+ $(GTLIBS) \
+ $(OVERRIDELIBS)))
+
+ $(eval $(call PROGRAM_template, bin/examples/custom_stream, \
+ obj/src/examples/custom_stream.o \
+ lib/libgenometools.a \
++$(ADDITIONAL_STATIC_DEPS) \
+ $(OVERRIDELIBS)))
+
+ $(eval $(call PROGRAM_template, bin/examples/gff3sort, \
+ obj/src/examples/gff3sort.o \
+
[med-svn] r11649 - in trunk/packages/genometools/trunk/debian: . patches
Author: sascha-guest Date: 2012-07-09 12:35:27 + (Mon, 09 Jul 2012) New Revision: 11649 Modified: trunk/packages/genometools/trunk/debian/changelog trunk/packages/genometools/trunk/debian/patches/adding_soname trunk/packages/genometools/trunk/debian/patches/libbam-fix Log: update to 1.4.1 Modified: trunk/packages/genometools/trunk/debian/changelog === --- trunk/packages/genometools/trunk/debian/changelog 2012-07-09 11:40:22 UTC (rev 11648) +++ trunk/packages/genometools/trunk/debian/changelog 2012-07-09 12:35:27 UTC (rev 11649) @@ -1,3 +1,11 @@ +genometools (1.4.1-1) unstable; urgency=low + + * New upstream release (1.4.1) + * the GFF3 parser now handles children which are defined before their parents + * many small improvements to the GFF3 parser + + -- Sascha Steinbiss Mon, 09 Jul 2012 14:10:23 +0100 + genometools (1.4.0-1) unstable; urgency=low * Initial release (Closes: #657923) Modified: trunk/packages/genometools/trunk/debian/patches/adding_soname === --- trunk/packages/genometools/trunk/debian/patches/adding_soname 2012-07-09 11:40:22 UTC (rev 11648) +++ trunk/packages/genometools/trunk/debian/patches/adding_soname 2012-07-09 12:35:27 UTC (rev 11649) @@ -1,16 +1,14 @@ -Index: genometools-1.4.0/Makefile -=== genometools-1.4.0.orig/Makefile2012-03-26 16:46:06.0 +0200 -+++ genometools-1.4.0/Makefile 2012-03-26 16:47:21.0 +0200 -@@ -78,6 +78,7 @@ +--- genometools-1.4.1.orig/Makefile genometools-1.4.1/Makefile +@@ -77,6 +77,7 @@ SHARED_OBJ_NAME_EXT:=.so SHARED:=-shared endif +SONAME_VERSION:=.0 # libraries for which we build replacements (that also appear in dependencies) - OVERRIDELIBS:=-lbz2 -lz -@@ -233,7 +234,7 @@ + EXP_LDLIBS+=-lz -lbz2 +@@ -235,7 +236,7 @@ # add necessary shared lib dependencies then not building them ourselves ifeq ($(useshared),yes) @@ -19,7 +17,7 @@ -llua5.1-filesystem -llua5.1-des56 -lbam EXP_LDLIBS += $(DEPLIBS) GTSHAREDLIB_LIBDEP += $(DEPLIBS) -@@ -573,8 +574,8 @@ +@@ -538,8 +539,8 @@ $(ADDITIONAL_SO_DEPS) @echo "[link $(@F)]" @test -d $(@D) || mkdir -p $(@D) @@ -30,7 +28,7 @@ lib/libtecla.a: $(LIBTECLA_OBJ) @echo "[link $(@F)]" -@@ -918,7 +919,8 @@ +@@ -872,7 +873,8 @@ ifdef RANLIB $(RANLIB) $(prefix)/lib/libgenometools.a endif Modified: trunk/packages/genometools/trunk/debian/patches/libbam-fix === --- trunk/packages/genometools/trunk/debian/patches/libbam-fix 2012-07-09 11:40:22 UTC (rev 11648) +++ trunk/packages/genometools/trunk/debian/patches/libbam-fix 2012-07-09 12:35:27 UTC (rev 11649) @@ -1,6 +1,6 @@ genometools-1.4.0.orig/Makefile -+++ genometools-1.4.0/Makefile -@@ -235,7 +235,7 @@ +--- genometools-1.4.1.orig/Makefile genometools-1.4.1/Makefile +@@ -237,7 +237,7 @@ # add necessary shared lib dependencies then not building them ourselves ifeq ($(useshared),yes) DEPLIBS:=-lm -lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \ @@ -9,7 +9,7 @@ EXP_LDLIBS += $(DEPLIBS) GTSHAREDLIB_LIBDEP += $(DEPLIBS) endif -@@ -555,6 +555,10 @@ +@@ -520,6 +520,10 @@ @$(RANLIB) $@ endif @@ -20,7 +20,7 @@ lib/libgenometools.a: obj/gt_config.h $(LIBGENOMETOOLS_OBJ) @echo "[link $(@F)]" @test -d $(@D) || mkdir -p $(@D) -@@ -563,19 +567,13 @@ +@@ -528,19 +532,13 @@ @$(RANLIB) $@ endif @@ -42,7 +42,7 @@ lib/libtecla.a: $(LIBTECLA_OBJ) @echo "[link $(@F)]" -@@ -603,48 +601,62 @@ +@@ -568,48 +566,62 @@ $(eval $(call PROGRAM_template, bin/skproto, $(SKPROTO_OBJ) \ lib/libgenometools.a\ ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11682 - trunk/packages/genometools/trunk/debian
Author: sascha-guest
Date: 2012-07-10 08:41:25 + (Tue, 10 Jul 2012)
New Revision: 11682
Modified:
trunk/packages/genometools/trunk/debian/control
Log:
minor textual changes
Modified: trunk/packages/genometools/trunk/debian/control
===
--- trunk/packages/genometools/trunk/debian/control 2012-07-10 08:25:54 UTC
(rev 11681)
+++ trunk/packages/genometools/trunk/debian/control 2012-07-10 08:41:25 UTC
(rev 11682)
@@ -3,8 +3,9 @@
Priority: extra
Maintainer: Sascha Steinbiss
Build-Depends: debhelper (>= 7.0.50~),
- liblua5.1-0-dev, liblua5.1-md5-dev, liblua5.1-filesystem-dev,
liblua5.1-lpeg-dev,
- libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, libncurses5-dev,
libsqlite3-dev, libbam-dev
+ liblua5.1-0-dev, liblua5.1-md5-dev, liblua5.1-filesystem-dev,
+ liblua5.1-lpeg-dev, libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev,
+ libncurses5-dev, libsqlite3-dev, libbam-dev
Standards-Version: 3.9.3
Homepage: http://genometools.org
Vcs-Browser:
http://svn.debian.org/viewvc/debian-med/trunk/packages/genometools/trunk/
@@ -17,13 +18,15 @@
The GenomeTools contains a collection of useful tools for biological
sequence analysis and -presentation combined into a single binary.
.
- The toolkit contains binaries for sequence and annotation handling,
- index structure generation and access, efficient matching, annotation
- visualization and much more.
+ The toolkit contains binaries for sequence and annotation handling, sequence
+ compression, index structure generation and access, annotation visualization,
+ and much more.
Package: genometools-common
Architecture: all
-Depends: ${misc:Depends}, liblua5.1-md5-0|liblua5.1-0,
liblua5.1-lpeg2|liblua5.1-0, liblua5.1-filesystem0|liblua5.1-0, liblua5.1-0,
libcairo2, zlib1g, libbz2-1.0, libexpat1, libpth20, libncurses5, libsqlite3-0
+Depends: ${misc:Depends}, liblua5.1-md5-0|liblua5.1-0,
+ liblua5.1-lpeg2|liblua5.1-0, liblua5.1-filesystem0|liblua5.1-0, liblua5.1-0,
+ libcairo2, zlib1g, libbz2-1.0, libexpat1, libpth20, libncurses5, libsqlite3-0
Description: shared data files for GenomeTools
This package contains configuration files such as alphabet
transformations, style files, etc. required to use the GenomeTools
@@ -38,17 +41,19 @@
via an object-oriented interface, and a collection of useful tools for
bioinformatics, combined into a single binary.
.
- The library contains components for sequence and annotation handling,
- index structure generation and access, efficient matching, annotation
- visualization and much more.
+ Besides basic bioinformatics data structures, the library contains components
+ for sequence and annotation handling, sequence compression, index structure
+ generation and access, efficient matching, annotation visualization and much
+ more.
Package: libgenometools0-dev
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, libgenometools0 (=
${binary:Version})
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ libgenometools0 (= ${binary:Version})
Section: libdevel
Description: development files for GenomeTools
This package contains the GenomeTools static libraries and necessary
- header files.
+ header files.
Package: genometools-doc
Architecture: all
___
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[med-svn] r11684 - in trunk/packages/genometools/trunk/debian: . patches
Author: sascha-guest
Date: 2012-07-10 09:09:19 + (Tue, 10 Jul 2012)
New Revision: 11684
Added:
trunk/packages/genometools/trunk/debian/patches/remove-gitignores
Removed:
trunk/packages/genometools/trunk/debian/patches/adding_soname.patch
Modified:
trunk/packages/genometools/trunk/debian/control
trunk/packages/genometools/trunk/debian/copyright
trunk/packages/genometools/trunk/debian/patches/series
Log:
clean up some issues
Modified: trunk/packages/genometools/trunk/debian/control
===
--- trunk/packages/genometools/trunk/debian/control 2012-07-10 08:49:42 UTC
(rev 11683)
+++ trunk/packages/genometools/trunk/debian/control 2012-07-10 09:09:19 UTC
(rev 11684)
@@ -65,7 +65,8 @@
Package: genometools-dbg
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, genometools-common
+Depends: ${shlibs:Depends}, ${misc:Depends},
+ genometools (= ${binary:Version})|libgenometools0 (= ${binary:Version})
Section: debug
Description: versatile genome analysis toolkit, with debug symbols
This package contains debug information stripped from the GenomeTools.
Modified: trunk/packages/genometools/trunk/debian/copyright
===
--- trunk/packages/genometools/trunk/debian/copyright 2012-07-10 08:49:42 UTC
(rev 11683)
+++ trunk/packages/genometools/trunk/debian/copyright 2012-07-10 09:09:19 UTC
(rev 11684)
@@ -21,7 +21,7 @@
Permission to use, copy, modify, and distribute this software for any
purpose with or without fee is hereby granted, provided that the above
copyright notice and this permission notice appear in all copies.
-
+
THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
@@ -57,7 +57,7 @@
copyright notice(s) and this permission notice appear in all copies of
the Software and that both the above copyright notice(s) and this
permission notice appear in supporting documentation.
-
+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT
@@ -67,7 +67,7 @@
FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
-
+
Except as contained in this notice, the name of a copyright holder
shall not be used in advertising or otherwise to promote the sale, use
or other dealings in this Software without prior written authorization
@@ -91,7 +91,7 @@
3. Neither the name of the University nor the names of its contributors
may be used to endorse or promote products derived from this software
without specific prior written permission.
-
+
THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
@@ -114,7 +114,7 @@
http://eternallyconfuzzled.com/tuts/datastructures/jsw_tut_rbtree.aspx
> Created (Julienne Walker): August 23, 2003
> Modified (Julienne Walker): March 14, 2008
-
+
Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to deal in the Software without
@@ -123,10 +123,10 @@
copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following
conditions:
-
+
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
-
+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
Deleted: trunk/packages/genometools/trunk/debian/patches/adding_soname.patch
===
--- trunk/packages/genometools/trunk/debian/patches/adding_soname.patch
2012-07-10 08:49:42 UTC (rev 11683)
+++ trunk/packages/genometools/trunk/debian/patches/adding_soname.patch
2012-07-10 09:09:19 UTC (rev 11684)
@@ -1,42 +0,0 @@
-Index: genometools-1.3.9/Makefile
-===
genometools-1.3.9.orig/Makefile2012-01-30 00:13:54.238911009 +0100
-+++ genometools-1.3.9/Makefile 2012-01-30 00:12:33.530510798 +0100
-@@ -79,6 +79,7 @@
- SHARED_OBJ_NAME_EXT:=.so
- SHARED:=-shared
- endif
-+SONAME_VERSION:=.0
-
- # libraries for which we build replacements (that also appear in dependencies)
- EXP_LDLIBS+=-lz -lbz2
-@@ -228,7 +229,7 @
[med-svn] r11685 - trunk/packages/genometools/trunk/debian
Author: sascha-guest Date: 2012-07-10 09:34:49 + (Tue, 10 Jul 2012) New Revision: 11685 Modified: trunk/packages/genometools/trunk/debian/copyright Log: properly format copyright lines Modified: trunk/packages/genometools/trunk/debian/copyright === --- trunk/packages/genometools/trunk/debian/copyright 2012-07-10 09:09:19 UTC (rev 11684) +++ trunk/packages/genometools/trunk/debian/copyright 2012-07-10 09:34:49 UTC (rev 11685) @@ -21,14 +21,14 @@ Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies. - + . THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF - OR IN CONNECTION WITH THE USE OR PERqFORMANCE OF THIS SOFTWARE. + OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. Files: src/core/yarandom.* @@ -57,7 +57,7 @@ copyright notice(s) and this permission notice appear in all copies of the Software and that both the above copyright notice(s) and this permission notice appear in supporting documentation. - + . THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT @@ -67,7 +67,7 @@ FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. - + . Except as contained in this notice, the name of a copyright holder shall not be used in advertising or otherwise to promote the sale, use or other dealings in this Software without prior written authorization @@ -91,7 +91,7 @@ 3. Neither the name of the University nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. - + . THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE @@ -108,13 +108,12 @@ src/extended/rbtree.[ch] Copyright: Copyright (c) 2009 Charles Wilson - License: Derived from code released into the public domain by Julienne Walker: http://eternallyconfuzzled.com/tuts/datastructures/jsw_tut_rbtree.aspx > Created (Julienne Walker): August 23, 2003 > Modified (Julienne Walker): March 14, 2008 - + . Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without @@ -123,10 +122,10 @@ copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: - + . The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. - + . THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11689 - trunk/packages/genometools/trunk/debian/patches
Author: sascha-guest Date: 2012-07-10 12:53:15 + (Tue, 10 Jul 2012) New Revision: 11689 Modified: trunk/packages/genometools/trunk/debian/patches/adding_soname trunk/packages/genometools/trunk/debian/patches/libbam-fix Log: clean up some lintian issues Modified: trunk/packages/genometools/trunk/debian/patches/adding_soname === --- trunk/packages/genometools/trunk/debian/patches/adding_soname 2012-07-10 12:35:48 UTC (rev 11688) +++ trunk/packages/genometools/trunk/debian/patches/adding_soname 2012-07-10 12:53:15 UTC (rev 11689) @@ -23,7 +23,7 @@ @test -d $(@D) || mkdir -p $(@D) - @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(SHARED) $(LIBGENOMETOOLS_OBJ) \ - -o $@ $(GTSHAREDLIB_LIBDEP) -+ @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(SHARED) -Wl,-soname,$(notdir $@) $(LIBGENOMETOOLS_OBJ) \ ++ @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(SHARED) -Wl,-soname,$(notdir $@)$(SONAME_VERSION) $(LIBGENOMETOOLS_OBJ) \ + -o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP) lib/libtecla.a: $(LIBTECLA_OBJ) Modified: trunk/packages/genometools/trunk/debian/patches/libbam-fix === --- trunk/packages/genometools/trunk/debian/patches/libbam-fix 2012-07-10 12:35:48 UTC (rev 11688) +++ trunk/packages/genometools/trunk/debian/patches/libbam-fix 2012-07-10 12:53:15 UTC (rev 11689) @@ -20,7 +20,7 @@ lib/libgenometools.a: obj/gt_config.h $(LIBGENOMETOOLS_OBJ) @echo "[link $(@F)]" @test -d $(@D) || mkdir -p $(@D) -@@ -528,19 +532,13 @@ +@@ -528,19 +532,14 @@ @$(RANLIB) $@ endif @@ -36,13 +36,15 @@ + $(ADDITIONAL_STATIC_DEPS) @echo "[link $(@F)]" @test -d $(@D) || mkdir -p $(@D) - @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(SHARED) -Wl,-soname,$(notdir $@) $(LIBGENOMETOOLS_OBJ) \ +- @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(SHARED) -Wl,-soname,$(notdir $@)$(SONAME_VERSION) $(LIBGENOMETOOLS_OBJ) \ - -o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP) -+ -o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP) $(ADDITIONAL_STATIC_DEPS) ++ @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(SHARED) \ ++-Wl,-soname,$(notdir $@)$(SONAME_VERSION) $(LIBGENOMETOOLS_OBJ) \ ++-o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP) $(ADDITIONAL_STATIC_DEPS) lib/libtecla.a: $(LIBTECLA_OBJ) @echo "[link $(@F)]" -@@ -568,48 +566,62 @@ +@@ -568,48 +567,62 @@ $(eval $(call PROGRAM_template, bin/skproto, $(SKPROTO_OBJ) \ lib/libgenometools.a\ @@ -109,3 +111,12 @@ bin/lua: $(LUAMAIN_OBJ) @echo "[link $(@F)]" +@@ -709,7 +722,7 @@ + @echo "[compile $$(@F)]" + @test -d $$(@D) || mkdir -p $$(@D) + @$$(CC) -c $$< -o $$@ $$(EXP_CPPFLAGS) $$(GT_CPPFLAGS) $$(EXP_CFLAGS) \ +-$$(GT_CFLAGS) $(3) ++$$(GT_CFLAGS) $(3) + @$$(CC) -c $$< -o $$(@:.o=.d) $$(EXP_CPPFLAGS) $$(GT_CPPFLAGS) \ + $(3) -MM -MP -MT $$@ + endef ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11691 - trunk/packages/genometools/trunk/debian/patches
Author: sascha-guest Date: 2012-07-10 13:10:13 + (Tue, 10 Jul 2012) New Revision: 11691 Added: trunk/packages/genometools/trunk/debian/patches/add-hardening Modified: trunk/packages/genometools/trunk/debian/patches/series Log: modify CFLAGS and friends for package building Added: trunk/packages/genometools/trunk/debian/patches/add-hardening === --- trunk/packages/genometools/trunk/debian/patches/add-hardening (rev 0) +++ trunk/packages/genometools/trunk/debian/patches/add-hardening 2012-07-10 13:10:13 UTC (rev 11691) @@ -0,0 +1,11 @@ +--- genometools-1.4.1.orig/Makefile genometools-1.4.1/Makefile +@@ -25,6 +25,8 @@ + -I$(CURDIR)/src/external/bzip2-1.0.6 \ + -I$(CURDIR)/src/external/libtecla-1.6.1 \ + -I$(CURDIR)/src/external/samtools-0.1.18 ++#Debian hardening ++CFLAGS+=`dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS` + # these variables are exported by the configuration script + ifndef CC + CC:=gcc Modified: trunk/packages/genometools/trunk/debian/patches/series === --- trunk/packages/genometools/trunk/debian/patches/series 2012-07-10 13:02:16 UTC (rev 11690) +++ trunk/packages/genometools/trunk/debian/patches/series 2012-07-10 13:10:13 UTC (rev 11691) @@ -1,3 +1,4 @@ +add-hardening adding_soname libbam-fix remove-gitignores ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11723 - trunk/packages/genometools/trunk/debian
Author: sascha-guest Date: 2012-07-11 09:58:13 + (Wed, 11 Jul 2012) New Revision: 11723 Modified: trunk/packages/genometools/trunk/debian/rules Log: remove debug line Modified: trunk/packages/genometools/trunk/debian/rules === --- trunk/packages/genometools/trunk/debian/rules 2012-07-11 09:47:03 UTC (rev 11722) +++ trunk/packages/genometools/trunk/debian/rules 2012-07-11 09:58:13 UTC (rev 11723) @@ -12,13 +12,12 @@ endif %: - dh $@ --parallel + dh $@ --parallel override_dh_auto_clean: $(MAKE) cleanup -override_dh_auto_build: - echo $(DEB_BUILD_ARCH_BITS) +override_dh_auto_build: dh_auto_build -- useshared=yes 64bit=$(64BIT) override_dh_auto_test: ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11724 - in trunk/packages/genometools/trunk/debian: . patches
Author: sascha-guest Date: 2012-07-11 11:23:00 + (Wed, 11 Jul 2012) New Revision: 11724 Modified: trunk/packages/genometools/trunk/debian/compat trunk/packages/genometools/trunk/debian/control trunk/packages/genometools/trunk/debian/patches/series trunk/packages/genometools/trunk/debian/rules Log: use debhelper 9, make sure that external CFLAGS are honored Modified: trunk/packages/genometools/trunk/debian/compat === --- trunk/packages/genometools/trunk/debian/compat 2012-07-11 09:58:13 UTC (rev 11723) +++ trunk/packages/genometools/trunk/debian/compat 2012-07-11 11:23:00 UTC (rev 11724) @@ -1 +1 @@ -7 +9 Modified: trunk/packages/genometools/trunk/debian/control === --- trunk/packages/genometools/trunk/debian/control 2012-07-11 09:58:13 UTC (rev 11723) +++ trunk/packages/genometools/trunk/debian/control 2012-07-11 11:23:00 UTC (rev 11724) @@ -2,7 +2,7 @@ Section: science Priority: extra Maintainer: Sascha Steinbiss -Build-Depends: debhelper (>= 7.0.50~), +Build-Depends: debhelper (>= 9), liblua5.1-0-dev, liblua5.1-md5-dev, liblua5.1-filesystem-dev, liblua5.1-lpeg-dev, libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, libncurses5-dev, libsqlite3-dev, libbam-dev Modified: trunk/packages/genometools/trunk/debian/patches/series === --- trunk/packages/genometools/trunk/debian/patches/series 2012-07-11 09:58:13 UTC (rev 11723) +++ trunk/packages/genometools/trunk/debian/patches/series 2012-07-11 11:23:00 UTC (rev 11724) @@ -1,4 +1,3 @@ -add-hardening adding_soname libbam-fix remove-gitignores Modified: trunk/packages/genometools/trunk/debian/rules === --- trunk/packages/genometools/trunk/debian/rules 2012-07-11 09:58:13 UTC (rev 11723) +++ trunk/packages/genometools/trunk/debian/rules 2012-07-11 11:23:00 UTC (rev 11724) @@ -18,13 +18,13 @@ $(MAKE) cleanup override_dh_auto_build: - dh_auto_build -- useshared=yes 64bit=$(64BIT) + dh_auto_build -- useshared=yes 64bit=$(64BIT) opt=no errorcheck=no override_dh_auto_test: #dh_auto_test -- useshared=yes 64bit=$(64BIT) testthreads=5 override_dh_auto_install: - dh_auto_install -- useshared=yes 64bit=$(64BIT) prefix=$(DESTDIR)/usr + dh_auto_install -- useshared=yes 64bit=$(64BIT) opt=no errorcheck=no prefix=$(DESTDIR)/usr override_dh_strip: dh_strip --dbg-package=genometools-dbg ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11725 - trunk/packages/genometools/trunk/debian
Author: sascha-guest Date: 2012-07-11 11:25:17 + (Wed, 11 Jul 2012) New Revision: 11725 Modified: trunk/packages/genometools/trunk/debian/libgenometools0-dev.install Log: remove static lib from dev package Modified: trunk/packages/genometools/trunk/debian/libgenometools0-dev.install === --- trunk/packages/genometools/trunk/debian/libgenometools0-dev.install 2012-07-11 11:23:00 UTC (rev 11724) +++ trunk/packages/genometools/trunk/debian/libgenometools0-dev.install 2012-07-11 11:25:17 UTC (rev 11725) @@ -1,2 +1 @@ usr/include -lib/libgenometools.a usr/lib ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11726 - trunk/packages/genometools/trunk/debian
Author: sascha-guest Date: 2012-07-11 11:28:33 + (Wed, 11 Jul 2012) New Revision: 11726 Added: trunk/packages/genometools/trunk/debian/libgenometools0-dev.links Removed: trunk/packages/genometools/trunk/debian/libgenometools0.links Log: move library symlink to dev package Added: trunk/packages/genometools/trunk/debian/libgenometools0-dev.links === --- trunk/packages/genometools/trunk/debian/libgenometools0-dev.links (rev 0) +++ trunk/packages/genometools/trunk/debian/libgenometools0-dev.links 2012-07-11 11:28:33 UTC (rev 11726) @@ -0,0 +1 @@ +usr/lib/libgenometools.so.0 usr/lib/libgenometools.so Deleted: trunk/packages/genometools/trunk/debian/libgenometools0.links === --- trunk/packages/genometools/trunk/debian/libgenometools0.links 2012-07-11 11:25:17 UTC (rev 11725) +++ trunk/packages/genometools/trunk/debian/libgenometools0.links 2012-07-11 11:28:33 UTC (rev 11726) @@ -1 +0,0 @@ -usr/lib/libgenometools.so.0 usr/lib/libgenometools.so ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11924 - trunk/packages/genometools/trunk/debian
Author: sascha-guest Date: 2012-07-28 09:38:09 + (Sat, 28 Jul 2012) New Revision: 11924 Modified: trunk/packages/genometools/trunk/debian/changelog trunk/packages/genometools/trunk/debian/copyright trunk/packages/genometools/trunk/debian/rules Log: address issues raised by ftpmaster Modified: trunk/packages/genometools/trunk/debian/changelog === --- trunk/packages/genometools/trunk/debian/changelog 2012-07-27 20:44:53 UTC (rev 11923) +++ trunk/packages/genometools/trunk/debian/changelog 2012-07-28 09:38:09 UTC (rev 11924) @@ -1,4 +1,4 @@ -genometools (1.4.1-1) UNRELEASED; urgency=low +genometools (1.4.1-1) unstable; urgency=low * Initial release (Closes: #657923) * the GFF3 parser now handles children which are defined before their parents Modified: trunk/packages/genometools/trunk/debian/copyright === --- trunk/packages/genometools/trunk/debian/copyright 2012-07-27 20:44:53 UTC (rev 11923) +++ trunk/packages/genometools/trunk/debian/copyright 2012-07-28 09:38:09 UTC (rev 11924) @@ -9,14 +9,19 @@ 2003-2012 Gordon Gremme 2007-2012 Sascha Steinbiss 2004-2012 Stefan Bienert + 2010-2011 Joachim Bonnet 2007 David Ellinghaus + 2008 Johannes Fischer 2009-2012 Giorgio Gonnella 2007-2008 Thomas Jahns 2007 Malte Mader 2009 Brent Pedersen 2007 Christin Schaerfer 2007 David Schmitz-Huebsch + 2003-2005 Michael E Sparks + 2009 Zhihao Tang 2010-2012 Dirk Willrodt + 2004-2012 Center for Bioinformatics, University of Hamburg License: Permission to use, copy, modify, and distribute this software for any purpose with or without fee is hereby granted, provided that the above Modified: trunk/packages/genometools/trunk/debian/rules === --- trunk/packages/genometools/trunk/debian/rules 2012-07-27 20:44:53 UTC (rev 11923) +++ trunk/packages/genometools/trunk/debian/rules 2012-07-28 09:38:09 UTC (rev 11924) @@ -24,10 +24,10 @@ #dh_auto_test -- useshared=yes 64bit=$(64BIT) testthreads=5 override_dh_auto_install: - dh_auto_install -- useshared=yes 64bit=$(64BIT) opt=no errorcheck=no prefix=$(DESTDIR)/usr + dh_auto_install --exclude=cgilua -- useshared=yes 64bit=$(64BIT) opt=no errorcheck=no prefix=$(DESTDIR)/usr override_dh_strip: dh_strip --dbg-package=genometools-dbg override_dh_installdocs: - dh_installdocs --exclude=license.template + dh_installdocs --exclude=license.template --exclude=lgpl.txt ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r11925 - trunk/packages/genometools/trunk/debian
Author: sascha-guest Date: 2012-07-28 09:55:24 + (Sat, 28 Jul 2012) New Revision: 11925 Modified: trunk/packages/genometools/trunk/debian/genometools-common.install trunk/packages/genometools/trunk/debian/rules Log: make sure that cgilua is not installed Modified: trunk/packages/genometools/trunk/debian/genometools-common.install === --- trunk/packages/genometools/trunk/debian/genometools-common.install 2012-07-28 09:38:09 UTC (rev 11924) +++ trunk/packages/genometools/trunk/debian/genometools-common.install 2012-07-28 09:55:24 UTC (rev 11925) @@ -1,3 +1,16 @@ -usr/bin/gtdata usr/share/genometools/ +usr/bin/gtdata/doc usr/share/genometools/gtdata +usr/bin/gtdata/obo_files usr/share/genometools/gtdata +usr/bin/gtdata/sketch usr/share/genometools/gtdata +usr/bin/gtdata/trans usr/share/genometools/gtdata +usr/bin/gtdata/modules/fileutils.lua usr/share/genometools/gtdata/modules +usr/bin/gtdata/modules/gtdoclib.lua usr/share/genometools/gtdata/modules +usr/bin/gtdata/modules/gtdoclib usr/share/genometools/gtdata/modules +usr/bin/gtdata/modules/gtlua.lua usr/share/genometools/gtdata/modules +usr/bin/gtdata/modules/gtlua usr/share/genometools/gtdata/modules +usr/bin/gtdata/modules/gtmodulehelper.lua usr/share/genometools/gtdata/modules +usr/bin/gtdata/modules/stringext.lua usr/share/genometools/gtdata/modules +usr/bin/gtdata/modules/warning.lua usr/share/genometools/gtdata/modules +usr/bin/gtdata/modules/gtlua.lua usr/share/genometools/gtdata/modules +usr/bin/gtdata/modules/external/md5.lua usr/share/genometools/gtdata/modules/external +usr/bin/gtdata/modules/external/re.lua usr/share/genometools/gtdata/modules/external - Modified: trunk/packages/genometools/trunk/debian/rules === --- trunk/packages/genometools/trunk/debian/rules 2012-07-28 09:38:09 UTC (rev 11924) +++ trunk/packages/genometools/trunk/debian/rules 2012-07-28 09:55:24 UTC (rev 11925) @@ -18,13 +18,13 @@ $(MAKE) cleanup override_dh_auto_build: - dh_auto_build -- useshared=yes 64bit=$(64BIT) opt=no errorcheck=no + dh_auto_build --parallel -- useshared=yes 64bit=$(64BIT) opt=no errorcheck=no override_dh_auto_test: #dh_auto_test -- useshared=yes 64bit=$(64BIT) testthreads=5 override_dh_auto_install: - dh_auto_install --exclude=cgilua -- useshared=yes 64bit=$(64BIT) opt=no errorcheck=no prefix=$(DESTDIR)/usr + dh_auto_install -- useshared=yes 64bit=$(64BIT) opt=no errorcheck=no prefix=$(DESTDIR)/usr override_dh_strip: dh_strip --dbg-package=genometools-dbg ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r12318 - in trunk/packages/genometools/trunk/debian: . patches
Author: sascha-guest Date: 2012-10-05 14:07:42 + (Fri, 05 Oct 2012) New Revision: 12318 Modified: trunk/packages/genometools/trunk/debian/changelog trunk/packages/genometools/trunk/debian/patches/adding_soname trunk/packages/genometools/trunk/debian/patches/libbam-fix trunk/packages/genometools/trunk/debian/patches/remove-gitignores Log: new upstream release 1.4.2 Modified: trunk/packages/genometools/trunk/debian/changelog === --- trunk/packages/genometools/trunk/debian/changelog 2012-10-05 13:36:54 UTC (rev 12317) +++ trunk/packages/genometools/trunk/debian/changelog 2012-10-05 14:07:42 UTC (rev 12318) @@ -1,3 +1,9 @@ +genometools (1.4.2-1) unstable; urgency=low + + * New upstream release + + -- Sascha Steinbiss Fri, 05 Oct 2012 15:47:56 +0200 + genometools (1.4.1-1) unstable; urgency=low * Initial release (Closes: #657923) Modified: trunk/packages/genometools/trunk/debian/patches/adding_soname === --- trunk/packages/genometools/trunk/debian/patches/adding_soname 2012-10-05 13:36:54 UTC (rev 12317) +++ trunk/packages/genometools/trunk/debian/patches/adding_soname 2012-10-05 14:07:42 UTC (rev 12318) @@ -1,34 +1,44 @@ genometools-1.4.1.orig/Makefile -+++ genometools-1.4.1/Makefile -@@ -77,6 +77,7 @@ +--- a/Makefile b/Makefile +@@ -86,6 +86,7 @@ SHARED_OBJ_NAME_EXT:=.so SHARED:=-shared endif +SONAME_VERSION:=.0 - # libraries for which we build replacements (that also appear in dependencies) - EXP_LDLIBS+=-lz -lbz2 -@@ -235,7 +236,7 @@ + # compiled executables + GTMAIN_SRC:=src/gt.c src/gtr.c src/gtt.c src/interactive.c +@@ -238,7 +239,7 @@ # add necessary shared lib dependencies then not building them ourselves ifeq ($(useshared),yes) -- DEPLIBS:=-lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \ -+ DEPLIBS:=-lm -lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \ +- DEPLIBS:=-lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \ ++ DEPLIBS:=-lm -lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \ -llua5.1-filesystem -llua5.1-des56 -lbam - EXP_LDLIBS += $(DEPLIBS) - GTSHAREDLIB_LIBDEP += $(DEPLIBS) -@@ -538,8 +539,8 @@ - $(ADDITIONAL_SO_DEPS) + else + DEPLIBS:= +@@ -517,7 +518,7 @@ + + ifdef DESTDIR + prefix:=$(DESTDIR)$(prefix) +-endif ++ endif + + # allow to set patch program + patch ?= patch +@@ -595,8 +596,9 @@ + $(ADDITIONAL_ZLIBS) @echo "[link $(@F)]" @test -d $(@D) || mkdir -p $(@D) -- @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(SHARED) $(LIBGENOMETOOLS_OBJ) \ +- @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(ADDITIONAL_SO_DEPS) $(SHARED) $(LIBGENOMETOOLS_OBJ) \ - -o $@ $(GTSHAREDLIB_LIBDEP) -+ @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(SHARED) -Wl,-soname,$(notdir $@)$(SONAME_VERSION) $(LIBGENOMETOOLS_OBJ) \ ++ @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $(ADDITIONAL_SO_DEPS) $(SHARED) \ ++ -Wl,-soname,$(notdir $@)$(SONAME_VERSION) $(LIBGENOMETOOLS_OBJ) \ + -o $@$(SONAME_VERSION) $(GTSHAREDLIB_LIBDEP) lib/libtecla.a: $(LIBTECLA_OBJ) @echo "[link $(@F)]" -@@ -872,7 +873,8 @@ +@@ -934,7 +936,8 @@ ifdef RANLIB $(RANLIB) $(prefix)/lib/libgenometools.a endif Modified: trunk/packages/genometools/trunk/debian/patches/libbam-fix === --- trunk/packages/genometools/trunk/debian/patches/libbam-fix 2012-10-05 13:36:54 UTC (rev 12317) +++ trunk/packages/genometools/trunk/debian/patches/libbam-fix 2012-10-05 14:07:42 UTC (rev 12318) @@ -1,15 +1,15 @@ genometools-1.4.1.orig/Makefile -+++ genometools-1.4.1/Makefile -@@ -237,7 +237,7 @@ +--- a/Makefile b/Makefile +@@ -240,7 +240,7 @@ # add necessary shared lib dependencies then not building them ourselves ifeq ($(useshared),yes) - DEPLIBS:=-lm -lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \ + DEPLIBS:=-lm -lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \ - -llua5.1-filesystem -llua5.1-des56 -lbam + -llua5.1-filesystem -llua5.1-des56 - EXP_LDLIBS += $(DEPLIBS) - GTSHAREDLIB_LIBDEP += $(DEPLIBS) + else + DEPLIBS:= endif -@@ -520,6 +520,10 @@ +@@ -576,6 +576,10 @@ @$(RANLIB) $@ endif @@ -20,103 +20,81 @@ lib/libgenometools.a: obj/gt_config.h $(LIBGENOMETOOLS_OBJ) @echo "[link $(@F)]" @test -d $(@D) || mkdir -p $(@D) -@@ -528,19 +532,14 @@ - @$(RANLIB) $@ - endif - --ifneq ($(useshared),yes) -- ADDITIONAL_SO_DEPS:=lib/libbz2.a \ -- lib/libexpat.a \ -- lib/libz.a --endif -- +@@ -593,12 +597,13 @@ lib/libgenometools$(SHARED_OBJ_NAME_EXT): obj/gt_config.h \
[med-svn] r12319 - trunk/packages/genometools/trunk/debian
Author: sascha-guest Date: 2012-10-06 21:20:07 + (Sat, 06 Oct 2012) New Revision: 12319 Added: trunk/packages/genometools/trunk/debian/upstream Log: add upstream file Added: trunk/packages/genometools/trunk/debian/upstream === --- trunk/packages/genometools/trunk/debian/upstream (rev 0) +++ trunk/packages/genometools/trunk/debian/upstream2012-10-06 21:20:07 UTC (rev 12319) @@ -0,0 +1,8 @@ +Name: GenomeTools +Bug-Database: http://genometools.lighthouseapp.com/tickets +Bug-Submit: http://genometools.lighthouseapp.com/projects/17855-genometools/tickets/new +Contact: Sascha Steinbiss +Homepage: http://genometools.org +Repository: git://genometools.org/genometools.git +Watch: | + http://genometools.org/pub/genometools-([0-9.]+)\.tar\.gz ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r12320 - in trunk/packages: . ltrsift ltrsift/trunk ltrsift/trunk/debian ltrsift/trunk/debian/source
Author: sascha-guest
Date: 2012-10-06 21:20:57 + (Sat, 06 Oct 2012)
New Revision: 12320
Added:
trunk/packages/ltrsift/
trunk/packages/ltrsift/trunk/
trunk/packages/ltrsift/trunk/debian/
trunk/packages/ltrsift/trunk/debian/changelog
trunk/packages/ltrsift/trunk/debian/compat
trunk/packages/ltrsift/trunk/debian/control
trunk/packages/ltrsift/trunk/debian/copyright
trunk/packages/ltrsift/trunk/debian/docs
trunk/packages/ltrsift/trunk/debian/ltrsift.docs
trunk/packages/ltrsift/trunk/debian/ltrsift.install
trunk/packages/ltrsift/trunk/debian/rules
trunk/packages/ltrsift/trunk/debian/source/
trunk/packages/ltrsift/trunk/debian/source/format
trunk/packages/ltrsift/trunk/debian/upstream
trunk/packages/ltrsift/trunk/debian/watch
Log:
add initial package for LTRsift
Property changes on: trunk/packages/ltrsift/trunk/debian
___
Added: mergeWithUpstream
+ 1
Added: trunk/packages/ltrsift/trunk/debian/changelog
===
--- trunk/packages/ltrsift/trunk/debian/changelog
(rev 0)
+++ trunk/packages/ltrsift/trunk/debian/changelog 2012-10-06 21:20:57 UTC
(rev 12320)
@@ -0,0 +1,5 @@
+ltrsift (1.0.1-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #)
+
+ -- Sascha Steinbiss Sun, 06 Oct 2012 15:08:11
+0200
Added: trunk/packages/ltrsift/trunk/debian/compat
===
--- trunk/packages/ltrsift/trunk/debian/compat (rev 0)
+++ trunk/packages/ltrsift/trunk/debian/compat 2012-10-06 21:20:57 UTC (rev
12320)
@@ -0,0 +1 @@
+9
Added: trunk/packages/ltrsift/trunk/debian/control
===
--- trunk/packages/ltrsift/trunk/debian/control (rev 0)
+++ trunk/packages/ltrsift/trunk/debian/control 2012-10-06 21:20:57 UTC (rev
12320)
@@ -0,0 +1,32 @@
+Source: ltrsift
+Section: science
+Priority: extra
+Maintainer: Sascha Steinbiss
+Build-Depends: debhelper (>= 9), libgenometools0-dev (>= 1.4.2), libgtk2.0-dev,
+ libglib2.0-dev
+Standards-Version: 3.9.3
+Homepage: http://www.zbh.uni-hamburg.de/LTRsift
+Vcs-Browser:
http://svn.debian.org/viewvc/debian-med/trunk/packages/ltrsift/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/ltrsift/trunk/
+
+Package: ltrsift
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, libgenometools0 (>= 1.4.2),
libgtk2.0-0,
+ libglib2.0-0, last-align, ncbi-blast+
+Description: semi-automatic postprocessing of de novo predicted LTR
retrotransposon annotations
+ LTRsift is a graphical desktop tool for semi-automatic postprocessing of de
+ novo predicted LTR retrotransposon annotations, such as the ones generated by
+ LTRharvest and LTRdigest. Its user-friendly interface displays LTR
+ retrotransposon candidates, their putative families and their internal
+ structure in a hierarchical fashion, allowing the user to "sift" through the
+ sometimes large results of de novo prediction software. It also offers
+ customizable filtering and classification functionality.
+
+Package: ltrsift-dbg
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, ltrsift (= ${binary:Version})
+Section: debug
+Description: semi-automatic postprocessing of de novo predicted LTR
retrotransposon annotations, with debug symbols
+ This package contains debug information stripped from LTRsift.
+ You may decide to install it to help identifying issues, typically
+ to help communication with upstream developers.
Added: trunk/packages/ltrsift/trunk/debian/copyright
===
--- trunk/packages/ltrsift/trunk/debian/copyright
(rev 0)
+++ trunk/packages/ltrsift/trunk/debian/copyright 2012-10-06 21:20:57 UTC
(rev 12320)
@@ -0,0 +1,47 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: ltrsift
+Source: http://www.zbh.uni-hamburg.de/LTRsift
+
+Files: *
+Copyright: 2012 Sascha Steinbiss
+ 2012 Sascha Kastens
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licens
[med-svn] r12325 - trunk/packages/genometools/trunk/debian
Author: sascha-guest
Date: 2012-10-08 06:05:54 + (Mon, 08 Oct 2012)
New Revision: 12325
Modified:
trunk/packages/genometools/trunk/debian/changelog
trunk/packages/genometools/trunk/debian/control
Log:
fix libpango issues
Modified: trunk/packages/genometools/trunk/debian/changelog
===
--- trunk/packages/genometools/trunk/debian/changelog 2012-10-07 17:33:05 UTC
(rev 12324)
+++ trunk/packages/genometools/trunk/debian/changelog 2012-10-08 06:05:54 UTC
(rev 12325)
@@ -1,3 +1,10 @@
+genometools (1.4.2-2) unstable; urgency=low
+
+ * Fixed libpango-dev dependency
+ * Updated manpages
+
+ -- Sascha Steinbiss Mon, 08 Oct 2012 07:51:52
+0200
+
genometools (1.4.2-1) unstable; urgency=low
* New upstream release
Modified: trunk/packages/genometools/trunk/debian/control
===
--- trunk/packages/genometools/trunk/debian/control 2012-10-07 17:33:05 UTC
(rev 12324)
+++ trunk/packages/genometools/trunk/debian/control 2012-10-08 06:05:54 UTC
(rev 12325)
@@ -5,7 +5,7 @@
Build-Depends: debhelper (>= 9),
liblua5.1-0-dev, liblua5.1-md5-dev, liblua5.1-filesystem-dev,
liblua5.1-lpeg-dev, libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev,
- libncurses5-dev, libsqlite3-dev, libbam-dev
+ libncurses5-dev, libsqlite3-dev, libbam-dev, libpango1.0-dev
Standards-Version: 3.9.4
DM-Upload-Allowed: yes
Homepage: http://genometools.org
@@ -27,7 +27,8 @@
Architecture: all
Depends: ${misc:Depends}, liblua5.1-md5-0|liblua5.1-0,
liblua5.1-lpeg2|liblua5.1-0, liblua5.1-filesystem0|liblua5.1-0, liblua5.1-0,
- libcairo2, zlib1g, libbz2-1.0, libexpat1, libpth20, libncurses5, libsqlite3-0
+ libcairo2, zlib1g, libbz2-1.0, libexpat1, libpth20, libncurses5, libsqlite3-0,
+ libpango1.0-0
Description: shared data files for GenomeTools
This package contains configuration files such as alphabet
transformations, style files, etc. required to use the GenomeTools
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[med-svn] r12326 - in trunk/packages/ltrsift/trunk/debian: . man man-src
Author: sascha-guest
Date: 2012-10-08 07:03:43 + (Mon, 08 Oct 2012)
New Revision: 12326
Added:
trunk/packages/ltrsift/trunk/debian/DRAFT
trunk/packages/ltrsift/trunk/debian/ltrsift.manpages
trunk/packages/ltrsift/trunk/debian/man-src/
trunk/packages/ltrsift/trunk/debian/man-src/ltrsift.1.txt
trunk/packages/ltrsift/trunk/debian/man-src/ltrsift_encode.1.txt
trunk/packages/ltrsift/trunk/debian/man/
trunk/packages/ltrsift/trunk/debian/man/ltrsift.1
trunk/packages/ltrsift/trunk/debian/man/ltrsift_encode.1
Modified:
trunk/packages/ltrsift/trunk/debian/control
trunk/packages/ltrsift/trunk/debian/copyright
trunk/packages/ltrsift/trunk/debian/ltrsift.docs
trunk/packages/ltrsift/trunk/debian/ltrsift.install
Log:
add manpages
Added: trunk/packages/ltrsift/trunk/debian/DRAFT
===
--- trunk/packages/ltrsift/trunk/debian/DRAFT (rev 0)
+++ trunk/packages/ltrsift/trunk/debian/DRAFT 2012-10-08 07:03:43 UTC (rev
12326)
@@ -0,0 +1 @@
+This is a draft for an upcoming LTRsift package.
Modified: trunk/packages/ltrsift/trunk/debian/control
===
--- trunk/packages/ltrsift/trunk/debian/control 2012-10-08 06:05:54 UTC (rev
12325)
+++ trunk/packages/ltrsift/trunk/debian/control 2012-10-08 07:03:43 UTC (rev
12326)
@@ -13,7 +13,7 @@
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, libgenometools0 (>= 1.4.2),
libgtk2.0-0,
libglib2.0-0, last-align, ncbi-blast+
-Description: semi-automatic postprocessing of de novo predicted LTR
retrotransposon annotations
+Description: postprocessing of LTR retrotransposons
LTRsift is a graphical desktop tool for semi-automatic postprocessing of de
novo predicted LTR retrotransposon annotations, such as the ones generated by
LTRharvest and LTRdigest. Its user-friendly interface displays LTR
@@ -26,7 +26,7 @@
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, ltrsift (= ${binary:Version})
Section: debug
-Description: semi-automatic postprocessing of de novo predicted LTR
retrotransposon annotations, with debug symbols
+Description: postprocessing of LTR retrotransposons, with debug symbols
This package contains debug information stripped from LTRsift.
You may decide to install it to help identifying issues, typically
to help communication with upstream developers.
Modified: trunk/packages/ltrsift/trunk/debian/copyright
===
--- trunk/packages/ltrsift/trunk/debian/copyright 2012-10-08 06:05:54 UTC
(rev 12325)
+++ trunk/packages/ltrsift/trunk/debian/copyright 2012-10-08 07:03:43 UTC
(rev 12326)
@@ -21,27 +21,3 @@
.
On Debian systems, the complete text of the GNU General
Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
-
-# If you want to use GPL v2 or later for the /debian/* files use
-# the following clauses, or change it to suit. Delete these two lines
-Files: debian/*
-Copyright: 2012 Sascha Steinbiss
-License: GPL-2+
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
- .
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
- .
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>
- .
- On Debian systems, the complete text of the GNU General
- Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
-
-# Please also look if there are files or directories which have a
-# different copyright/license attached and list them here.
Modified: trunk/packages/ltrsift/trunk/debian/ltrsift.docs
===
--- trunk/packages/ltrsift/trunk/debian/ltrsift.docs2012-10-08 06:05:54 UTC
(rev 12325)
+++ trunk/packages/ltrsift/trunk/debian/ltrsift.docs2012-10-08 07:03:43 UTC
(rev 12326)
@@ -1,4 +1,2 @@
-CHANGELOG
README
-LICENSE
VERSION
Modified: trunk/packages/ltrsift/trunk/debian/ltrsift.install
===
--- trunk/packages/ltrsift/trunk/debian/ltrsift.install 2012-10-08 06:05:54 UTC
(rev 12325)
+++ trunk/packages/ltrsift/trunk/debian/ltrsift.install 2012-10-08 07:03:43 UTC
(rev 12326)
@@ -1,5 +1,9 @@
usr/bin/ltrsift
usr/bin/ltrsift_encode
-usr/sample_data usr/share/ltrsift
+usr/sample_data/clean_encseqs usr/share/ltrsift/sample_data/clean_encseqs
+usr/sample_data/prepare_encseqs usr/share/ltrsift/sample_data/prepare_en
[med-svn] r12330 - trunk/packages/ltrsift/trunk/debian
Author: sascha-guest
Date: 2012-10-08 10:14:39 + (Mon, 08 Oct 2012)
New Revision: 12330
Modified:
trunk/packages/ltrsift/trunk/debian/control
Log:
move soft deps into Recommends
Modified: trunk/packages/ltrsift/trunk/debian/control
===
--- trunk/packages/ltrsift/trunk/debian/control 2012-10-08 09:59:53 UTC (rev
12329)
+++ trunk/packages/ltrsift/trunk/debian/control 2012-10-08 10:14:39 UTC (rev
12330)
@@ -11,8 +11,9 @@
Package: ltrsift
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, libgenometools0 (>= 1.4.2),
libgtk2.0-0,
- libglib2.0-0, last-align, ncbi-blast+
+Depends: ${shlibs:Depends}, ${misc:Depends}, libgenometools0 (>= 1.4.2),
+ libgtk2.0-0, libglib2.0-0
+Recommends: last-align, ncbi-blast+
Description: postprocessing of LTR retrotransposons
LTRsift is a graphical desktop tool for semi-automatic postprocessing of de
novo predicted LTR retrotransposon annotations, such as the ones generated by
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[med-svn] r12332 - trunk/packages/ltrsift/trunk/debian
Author: sascha-guest
Date: 2012-10-08 13:12:31 + (Mon, 08 Oct 2012)
New Revision: 12332
Modified:
trunk/packages/ltrsift/trunk/debian/control
Log:
extend description
Modified: trunk/packages/ltrsift/trunk/debian/control
===
--- trunk/packages/ltrsift/trunk/debian/control 2012-10-08 12:15:27 UTC (rev
12331)
+++ trunk/packages/ltrsift/trunk/debian/control 2012-10-08 13:12:31 UTC (rev
12332)
@@ -14,7 +14,7 @@
Depends: ${shlibs:Depends}, ${misc:Depends}, libgenometools0 (>= 1.4.2),
libgtk2.0-0, libglib2.0-0
Recommends: last-align, ncbi-blast+
-Description: postprocessing of LTR retrotransposons
+Description: postprocessing and classification of LTR retrotransposons
LTRsift is a graphical desktop tool for semi-automatic postprocessing of de
novo predicted LTR retrotransposon annotations, such as the ones generated by
LTRharvest and LTRdigest. Its user-friendly interface displays LTR
@@ -27,7 +27,7 @@
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, ltrsift (= ${binary:Version})
Section: debug
-Description: postprocessing of LTR retrotransposons, with debug symbols
+Description: postprocessing and classification of LTR retrotransposons, with
debug symbols
This package contains debug information stripped from LTRsift.
You may decide to install it to help identifying issues, typically
to help communication with upstream developers.
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[med-svn] r12334 - trunk/packages/ltrsift/trunk/debian
Author: sascha-guest Date: 2012-10-08 13:36:05 + (Mon, 08 Oct 2012) New Revision: 12334 Modified: trunk/packages/ltrsift/trunk/debian/changelog Log: add WNPP bug # Modified: trunk/packages/ltrsift/trunk/debian/changelog === --- trunk/packages/ltrsift/trunk/debian/changelog 2012-10-08 13:34:03 UTC (rev 12333) +++ trunk/packages/ltrsift/trunk/debian/changelog 2012-10-08 13:36:05 UTC (rev 12334) @@ -1,5 +1,5 @@ ltrsift (1.0.1-1) UNRELEASED; urgency=low - * Initial release (Closes: #) + * Initial release (Closes: #689961) -- Sascha Steinbiss Sun, 06 Oct 2012 15:08:11 +0200 ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r12337 - trunk/packages/ltrsift/trunk/debian
Author: sascha-guest Date: 2012-10-08 13:57:53 + (Mon, 08 Oct 2012) New Revision: 12337 Modified: trunk/packages/ltrsift/trunk/debian/watch Log: make watchfile return a tarball Modified: trunk/packages/ltrsift/trunk/debian/watch === --- trunk/packages/ltrsift/trunk/debian/watch 2012-10-08 13:42:52 UTC (rev 12336) +++ trunk/packages/ltrsift/trunk/debian/watch 2012-10-08 13:57:53 UTC (rev 12337) @@ -1,2 +1,2 @@ version=3 -https://github.com/satta/ltrsift/tags .*/zipball/v(\d[\d\.]+) +http://githubredir.debian.net/github/satta/ltrsift /github/satta/ltrsift/v(\d[\d\.]+).tar.gz ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r12351 - trunk/packages/genometools/trunk/debian
Author: sascha-guest Date: 2012-10-09 10:28:19 + (Tue, 09 Oct 2012) New Revision: 12351 Modified: trunk/packages/genometools/trunk/debian/changelog Log: try to fix invalid libc version dependency Modified: trunk/packages/genometools/trunk/debian/changelog === --- trunk/packages/genometools/trunk/debian/changelog 2012-10-09 08:24:21 UTC (rev 12350) +++ trunk/packages/genometools/trunk/debian/changelog 2012-10-09 10:28:19 UTC (rev 12351) @@ -1,3 +1,15 @@ +genometools (1.4.2-4) unstable; urgency=low + + * Remove shlibs.local file + + -- Sascha Steinbiss Tue, 09 Oct 2012 12:24:17 +0200 + +genometools (1.4.2-3) unstable; urgency=low + + * Build with pbuilder to obtain reasonable libc dependency (>= 2.13) + + -- Sascha Steinbiss Tue, 09 Oct 2012 10:04:34 +0200 + genometools (1.4.2-2) unstable; urgency=low * Fixed libpango-dev dependency ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r12355 - trunk/packages/ltrsift/trunk/debian
Author: sascha-guest Date: 2012-10-09 19:28:48 + (Tue, 09 Oct 2012) New Revision: 12355 Added: trunk/packages/ltrsift/trunk/debian/dirs trunk/packages/ltrsift/trunk/debian/ltrsift.desktop trunk/packages/ltrsift/trunk/debian/ltrsift.menu trunk/packages/ltrsift/trunk/debian/ltrsift.svg trunk/packages/ltrsift/trunk/debian/ltrsift.xpm Modified: trunk/packages/ltrsift/trunk/debian/ltrsift.install Log: add menu and desktop entries, icons Added: trunk/packages/ltrsift/trunk/debian/dirs === --- trunk/packages/ltrsift/trunk/debian/dirs(rev 0) +++ trunk/packages/ltrsift/trunk/debian/dirs2012-10-09 19:28:48 UTC (rev 12355) @@ -0,0 +1,4 @@ +/usr/share/pixmaps +/usr/share/applications +usr/share/icons/hicolor/scalable/apps +usr/share/ltrsift Added: trunk/packages/ltrsift/trunk/debian/ltrsift.desktop === --- trunk/packages/ltrsift/trunk/debian/ltrsift.desktop (rev 0) +++ trunk/packages/ltrsift/trunk/debian/ltrsift.desktop 2012-10-09 19:28:48 UTC (rev 12355) @@ -0,0 +1,9 @@ +[Desktop Entry] +Version=1.0 +Type=Application +Terminal=false +Exec=/usr/bin/ltrsift +Name=LTRsift +Comment=A graphical tool for postprocessing and classification of LTR retrotransposons. +Categories=Biology;Science;Education; +Icon=ltrsift Modified: trunk/packages/ltrsift/trunk/debian/ltrsift.install === --- trunk/packages/ltrsift/trunk/debian/ltrsift.install 2012-10-09 16:08:51 UTC (rev 12354) +++ trunk/packages/ltrsift/trunk/debian/ltrsift.install 2012-10-09 19:28:48 UTC (rev 12355) @@ -1,9 +1,11 @@ usr/bin/ltrsift usr/bin/ltrsift_encode -usr/sample_data/clean_encseqs usr/share/ltrsift/sample_data/clean_encseqs -usr/sample_data/prepare_encseqs usr/share/ltrsift/sample_data/prepare_encseqs -usr/sample_data/dmel58.ltrd.gff3 usr/share/ltrsift/sample_data/dmel58.ltrd.gff3 -usr/sample_data/dmel-2L-chromosome-r5.8.fasta.gz usr/share/ltrsift/sample_data/dmel-2L-chromosome-r5.8.fasta.gz -usr/sample_data/README usr/share/ltrsift/sample_data/README +usr/sample_data/clean_encseqs usr/share/ltrsift/sample_data +usr/sample_data/prepare_encseqs usr/share/ltrsift/sample_data +usr/sample_data/dmel58.ltrd.gff3 usr/share/ltrsift/sample_data +usr/sample_data/dmel-2L-chromosome-r5.8.fasta.gz usr/share/ltrsift/sample_data +usr/sample_data/README usr/share/ltrsift/sample_data usr/filters usr/share/ltrsift - +debian/ltrsift.desktop usr/share/applications +debian/ltrsift.svg usr/share/icons/hicolor/scalable/apps +debian/ltrsift.xpm usr/share/pixmaps Added: trunk/packages/ltrsift/trunk/debian/ltrsift.menu === --- trunk/packages/ltrsift/trunk/debian/ltrsift.menu (rev 0) +++ trunk/packages/ltrsift/trunk/debian/ltrsift.menu2012-10-09 19:28:48 UTC (rev 12355) @@ -0,0 +1,5 @@ +?package(ltrsift): needs="X11" \ + section="Applications/Science/Biology" \ + title="LTRsift" \ + command="/usr/bin/ltrsift" \ + icon="/usr/share/pixmaps/ltrsift.xpm" Added: trunk/packages/ltrsift/trunk/debian/ltrsift.svg === --- trunk/packages/ltrsift/trunk/debian/ltrsift.svg (rev 0) +++ trunk/packages/ltrsift/trunk/debian/ltrsift.svg 2012-10-09 19:28:48 UTC (rev 12355) @@ -0,0 +1,532 @@ + + + +http://purl.org/dc/elements/1.1/"; + xmlns:cc="http://creativecommons.org/ns#"; + xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"; + xmlns:svg="http://www.w3.org/2000/svg"; + xmlns="http://www.w3.org/2000/svg"; + xmlns:xlink="http://www.w3.org/1999/xlink"; + xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"; + xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"; + inkscape:export-ydpi="240.0" + inkscape:export-xdpi="240.0" + inkscape:export-filename="/home/jimmac/gfx/novell/pdes/trunk/docs/BIGmime-text.png" + sodipodi:docname="familysearch.svg" + inkscape:version="0.48.2 r9819" + sodipodi:version="0.32" + id="svg249" + height="48.00px" + width="48.00px" + inkscape:output_extension="org.inkscape.output.svg.inkscape" + version="1.1"> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +image/svg+xml +http://purl.org/dc/
[med-svn] r12374 - in trunk/packages/genometools/trunk/debian: . man
Author: sascha-guest
Date: 2012-10-10 22:20:53 + (Wed, 10 Oct 2012)
New Revision: 12374
Added:
trunk/packages/genometools/trunk/debian/man/gt-csa.1
Modified:
trunk/packages/genometools/trunk/debian/control
trunk/packages/genometools/trunk/debian/man/gt-fingerprint.1
trunk/packages/genometools/trunk/debian/man/gt-hop.1
trunk/packages/genometools/trunk/debian/rules
Log:
minor lintian cleanups
Modified: trunk/packages/genometools/trunk/debian/control
===
--- trunk/packages/genometools/trunk/debian/control 2012-10-10 19:34:52 UTC
(rev 12373)
+++ trunk/packages/genometools/trunk/debian/control 2012-10-10 22:20:53 UTC
(rev 12374)
@@ -54,8 +54,13 @@
libgenometools0 (= ${binary:Version})
Section: libdevel
Description: development files for GenomeTools
- This package contains the GenomeTools static libraries and necessary
+ This package contains the GenomeTools static library and necessary
header files.
+ .
+ Besides basic bioinformatics data structures, the library contains components
+ for sequence and annotation handling, sequence compression, index structure
+ generation and access, efficient matching, annotation visualization and much
+ more.
Package: genometools-doc
Architecture: all
@@ -63,7 +68,9 @@
Section: doc
Description: documentation for GenomeTools
This package contains API documentation and tool documentation for
- GenomeTools.
+ GenomeTools. The GenomeTools toolkit contains binaries for sequence and
+ annotation handling, sequence compression, index structure generation and
+ access, annotation visualization, and much more.
Package: genometools-dbg
Architecture: any
Added: trunk/packages/genometools/trunk/debian/man/gt-csa.1
===
--- trunk/packages/genometools/trunk/debian/man/gt-csa.1
(rev 0)
+++ trunk/packages/genometools/trunk/debian/man/gt-csa.12012-10-10
22:20:53 UTC (rev 12374)
@@ -0,0 +1,142 @@
+'\" t
+.\" Title: gt-csa
+.\"Author: [see the "AUTHOR" section]
+.\" Generator: DocBook XSL Stylesheets v1.76.1
[med-svn] r12375 - trunk/packages/genometools/trunk/debian
Author: sascha-guest Date: 2012-10-10 23:32:05 + (Wed, 10 Oct 2012) New Revision: 12375 Added: trunk/packages/genometools/trunk/debian/genometools-doc.doc-base Modified: trunk/packages/genometools/trunk/debian/control trunk/packages/genometools/trunk/debian/genometools-doc.docs trunk/packages/genometools/trunk/debian/rules Log: properly build documentation and doc-base registration Modified: trunk/packages/genometools/trunk/debian/control === --- trunk/packages/genometools/trunk/debian/control 2012-10-10 22:20:53 UTC (rev 12374) +++ trunk/packages/genometools/trunk/debian/control 2012-10-10 23:32:05 UTC (rev 12375) @@ -5,7 +5,9 @@ Build-Depends: debhelper (>= 9), liblua5.1-0-dev, liblua5.1-md5-dev, liblua5.1-filesystem-dev, liblua5.1-lpeg-dev, libcairo2-dev, zlib1g-dev, libbz2-dev, libexpat1-dev, - libncurses5-dev, libsqlite3-dev, libbam-dev, libpango1.0-dev + libncurses5-dev, libsqlite3-dev, libbam-dev, libpango1.0-dev, + texlive-latex-base, texlive-latex-extra, texlive-fonts-extra, latex-xcolor, + texlive-fonts-recommended Standards-Version: 3.9.4 DM-Upload-Allowed: yes Homepage: http://genometools.org @@ -40,8 +42,7 @@ Description: versatile genome analysis library This package contains the GenomeTools shared library and header files. It offers efficient sequence analysis components, available - via an object-oriented interface, and a collection of useful tools for - bioinformatics, combined into a single binary. + via an object-oriented interface. . Besides basic bioinformatics data structures, the library contains components for sequence and annotation handling, sequence compression, index structure Added: trunk/packages/genometools/trunk/debian/genometools-doc.doc-base === --- trunk/packages/genometools/trunk/debian/genometools-doc.doc-base (rev 0) +++ trunk/packages/genometools/trunk/debian/genometools-doc.doc-base 2012-10-10 23:32:05 UTC (rev 12375) @@ -0,0 +1,14 @@ +Document: genometools-doc +Title: GenomeTools manuals +Author: GenomeTools Team +Abstract: User manuals for GenomeTools + The GenomeTools contains a collection of useful tools for biological + sequence analysis and -presentation combined into a single binary. + . + The toolkit contains binaries for sequence and annotation handling, sequence + compression, index structure generation and access, annotation visualization, + and much more. +Section: Science/Biology + +Format: PDF +Files: /usr/share/doc/genometools-doc/*.pdf.gz Modified: trunk/packages/genometools/trunk/debian/genometools-doc.docs === --- trunk/packages/genometools/trunk/debian/genometools-doc.docs 2012-10-10 22:20:53 UTC (rev 12374) +++ trunk/packages/genometools/trunk/debian/genometools-doc.docs 2012-10-10 23:32:05 UTC (rev 12375) @@ -1 +1,2 @@ -doc/* +doc/manuals/*.pdf +doc/devguide/devguide.pdf Modified: trunk/packages/genometools/trunk/debian/rules === --- trunk/packages/genometools/trunk/debian/rules 2012-10-10 22:20:53 UTC (rev 12374) +++ trunk/packages/genometools/trunk/debian/rules 2012-10-10 23:32:05 UTC (rev 12375) @@ -19,7 +19,7 @@ $(MAKE) cleanup override_dh_auto_build: - dh_auto_build --parallel -- useshared=yes 64bit=$(64BIT) opt=no errorcheck=no + dh_auto_build --parallel -- useshared=yes 64bit=$(64BIT) opt=no errorcheck=no docs manuals override_dh_auto_test: #dh_auto_test -- useshared=yes 64bit=$(64BIT) testthreads=5 @@ -29,6 +29,3 @@ override_dh_strip: dh_strip --dbg-package=genometools-dbg - -override_dh_installdocs: - dh_installdocs --exclude=license.template --exclude=lgpl.txt ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r12381 - trunk/packages/ltrsift/trunk/debian
Author: sascha-guest
Date: 2012-10-11 09:08:27 + (Thu, 11 Oct 2012)
New Revision: 12381
Added:
trunk/packages/ltrsift/trunk/debian/ltrsift-examples.examples
Removed:
trunk/packages/ltrsift/trunk/debian/docs
Modified:
trunk/packages/ltrsift/trunk/debian/control
trunk/packages/ltrsift/trunk/debian/ltrsift.install
Log:
move large example data into own package to avoid lintian warning
Modified: trunk/packages/ltrsift/trunk/debian/control
===
--- trunk/packages/ltrsift/trunk/debian/control 2012-10-11 08:43:33 UTC (rev
12380)
+++ trunk/packages/ltrsift/trunk/debian/control 2012-10-11 09:08:27 UTC (rev
12381)
@@ -29,7 +29,19 @@
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, ltrsift (= ${binary:Version})
Section: debug
+Priority: extra
Description: postprocessing and classification of LTR retrotransposons, with
debug symbols
This package contains debug information stripped from LTRsift.
You may decide to install it to help identifying issues, typically
to help communication with upstream developers.
+
+Package: ltrsift-examples
+Architecture: all
+Depends: ${misc:Depends}
+Suggests: ltrsift
+Description: example data for LTRsift
+ This package contains test sequences (gzipped FASTA) and annotations (GFF3)
+ from the Drosophila melanogaster (fruit fly) genome, to be used in an example
+ process of postprocessing and classification of newly detected LTR
+ retrotransposons. Scripts for using LTRsift to encode the sequences into a
+ format accepted by LTRsift are included as well.
Deleted: trunk/packages/ltrsift/trunk/debian/docs
===
--- trunk/packages/ltrsift/trunk/debian/docs2012-10-11 08:43:33 UTC (rev
12380)
+++ trunk/packages/ltrsift/trunk/debian/docs2012-10-11 09:08:27 UTC (rev
12381)
@@ -1 +0,0 @@
-README
Added: trunk/packages/ltrsift/trunk/debian/ltrsift-examples.examples
===
--- trunk/packages/ltrsift/trunk/debian/ltrsift-examples.examples
(rev 0)
+++ trunk/packages/ltrsift/trunk/debian/ltrsift-examples.examples
2012-10-11 09:08:27 UTC (rev 12381)
@@ -0,0 +1,5 @@
+sample_data/clean_encseqs
+sample_data/prepare_encseqs
+sample_data/dmel58.ltrd.gff3
+sample_data/dmel-2L-chromosome-r5.8.fasta.gz
+sample_data/README
Modified: trunk/packages/ltrsift/trunk/debian/ltrsift.install
===
--- trunk/packages/ltrsift/trunk/debian/ltrsift.install 2012-10-11 08:43:33 UTC
(rev 12380)
+++ trunk/packages/ltrsift/trunk/debian/ltrsift.install 2012-10-11 09:08:27 UTC
(rev 12381)
@@ -1,10 +1,5 @@
usr/bin/ltrsift
usr/bin/ltrsift_encode
-usr/sample_data/clean_encseqs usr/share/ltrsift/sample_data
-usr/sample_data/prepare_encseqs usr/share/ltrsift/sample_data
-usr/sample_data/dmel58.ltrd.gff3 usr/share/ltrsift/sample_data
-usr/sample_data/dmel-2L-chromosome-r5.8.fasta.gz usr/share/ltrsift/sample_data
-usr/sample_data/README usr/share/ltrsift/sample_data
usr/filters usr/share/ltrsift
debian/ltrsift.desktop usr/share/applications
debian/ltrsift.svg usr/share/icons/hicolor/scalable/apps
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[med-svn] r12397 - trunk/packages/ltrsift/trunk/debian
Author: sascha-guest Date: 2012-10-12 13:30:42 + (Fri, 12 Oct 2012) New Revision: 12397 Removed: trunk/packages/ltrsift/trunk/debian/DRAFT Log: remove DRAFT flag Deleted: trunk/packages/ltrsift/trunk/debian/DRAFT === --- trunk/packages/ltrsift/trunk/debian/DRAFT 2012-10-12 13:05:36 UTC (rev 12396) +++ trunk/packages/ltrsift/trunk/debian/DRAFT 2012-10-12 13:30:42 UTC (rev 12397) @@ -1 +0,0 @@ -This is a draft for an upcoming LTRsift package. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r12531 - trunk/packages/ltrsift/trunk/debian
Author: sascha-guest Date: 2012-11-12 11:08:38 + (Mon, 12 Nov 2012) New Revision: 12531 Modified: trunk/packages/ltrsift/trunk/debian/copyright Log: add copyright line Modified: trunk/packages/ltrsift/trunk/debian/copyright === --- trunk/packages/ltrsift/trunk/debian/copyright 2012-11-09 07:44:19 UTC (rev 12530) +++ trunk/packages/ltrsift/trunk/debian/copyright 2012-11-12 11:08:38 UTC (rev 12531) @@ -2,9 +2,11 @@ Upstream-Name: ltrsift Source: http://www.zbh.uni-hamburg.de/LTRsift -Files: * -Copyright: 2012 Sascha Steinbiss - 2012 Sascha Kastens +Files: + * +Copyright: + 2012 Sascha Steinbiss + 2012 Sascha Kastens License: GPL-2+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by @@ -21,3 +23,22 @@ . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". + +Files: + scripts/tar_root.sh +Copyright: + 2012 Sascha Steinbiss + 2012 Center for Bioinformatics, University of Hamburg +License: + Permission to use, copy, modify, and distribute this software for any + purpose with or without fee is hereby granted, provided that the above + copyright notice and this permission notice appear in all copies. + . + THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES + WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF + MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR + ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES + WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN + ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF + OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. + ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r12566 - trunk/packages/ltrsift/trunk/debian
Author: sascha-guest Date: 2012-11-23 15:21:08 + (Fri, 23 Nov 2012) New Revision: 12566 Modified: trunk/packages/ltrsift/trunk/debian/watch Log: update watchfile with contributed version Modified: trunk/packages/ltrsift/trunk/debian/watch === --- trunk/packages/ltrsift/trunk/debian/watch 2012-11-23 09:19:15 UTC (rev 12565) +++ trunk/packages/ltrsift/trunk/debian/watch 2012-11-23 15:21:08 UTC (rev 12566) @@ -1,2 +1,3 @@ version=3 -http://githubredir.debian.net/github/satta/ltrsift /github/satta/ltrsift/v(\d[\d\.]+).tar.gz +https://github.com/satta/ltrsift/tags .*/v?(\d.*)\.(?:tgz|tar\.(?:gz|bz2|xz)) +# Bart Martens Mon, 19 Nov 2012 18:59:06 + ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r12914 - in trunk/packages/genometools/trunk/debian: . patches
Author: sascha-guest Date: 2013-02-05 18:13:50 + (Tue, 05 Feb 2013) New Revision: 12914 Modified: trunk/packages/genometools/trunk/debian/changelog trunk/packages/genometools/trunk/debian/patches/adding_soname trunk/packages/genometools/trunk/debian/patches/libbam-fix Log: New upstream release 1.5.0 Modified: trunk/packages/genometools/trunk/debian/changelog === --- trunk/packages/genometools/trunk/debian/changelog 2013-02-05 09:23:24 UTC (rev 12913) +++ trunk/packages/genometools/trunk/debian/changelog 2013-02-05 18:13:50 UTC (rev 12914) @@ -1,3 +1,23 @@ +genometools (1.5.0-1) unstable; urgency=low + + * New upstream release + * bugfixes and cleanups + * development tool `gt sain' added to run an induced suffix array sorting +algorithm + * the -typecheck option in the `gt gff3` and `gt gff3validator` tools +now also validates parent (part-of) relationships, see -help output for +details + * new option -encseq besides -seqfile(s) and -regionmapping to select a +encseq index as a sequence source + * GtBioseq backend switched to GtEncseq + * GtSeqCol is now an interface, GtEncseqCol added + * GtRankedList added + * GtSNPAnnotatorStream and `gt snpper' tool added + * node sorting code is now aware of MD5 hash presence + * compatibility with old Pango versions inproved + + -- Sascha Steinbiss Tue, 05 Feb 2013 18:52:22 +0100 + genometools (1.4.2-4) unstable; urgency=low * Remove shlibs.local file Modified: trunk/packages/genometools/trunk/debian/patches/adding_soname === --- trunk/packages/genometools/trunk/debian/patches/adding_soname 2013-02-05 09:23:24 UTC (rev 12913) +++ trunk/packages/genometools/trunk/debian/patches/adding_soname 2013-02-05 18:13:50 UTC (rev 12914) @@ -1,6 +1,6 @@ --- a/Makefile +++ b/Makefile -@@ -86,6 +86,7 @@ +@@ -96,6 +96,7 @@ SHARED_OBJ_NAME_EXT:=.so SHARED:=-shared endif @@ -8,7 +8,7 @@ # compiled executables GTMAIN_SRC:=src/gt.c src/gtr.c src/gtt.c src/interactive.c -@@ -238,7 +239,7 @@ +@@ -249,7 +250,7 @@ # add necessary shared lib dependencies then not building them ourselves ifeq ($(useshared),yes) @@ -17,7 +17,7 @@ -llua5.1-filesystem -llua5.1-des56 -lbam else DEPLIBS:= -@@ -517,7 +518,7 @@ +@@ -532,7 +533,7 @@ ifdef DESTDIR prefix:=$(DESTDIR)$(prefix) @@ -26,7 +26,7 @@ # allow to set patch program patch ?= patch -@@ -595,8 +596,9 @@ +@@ -610,8 +611,9 @@ $(ADDITIONAL_ZLIBS) @echo "[link $(@F)]" @test -d $(@D) || mkdir -p $(@D) @@ -38,7 +38,7 @@ lib/libtecla.a: $(LIBTECLA_OBJ) @echo "[link $(@F)]" -@@ -934,7 +936,8 @@ +@@ -950,7 +952,8 @@ ifdef RANLIB $(RANLIB) $(prefix)/lib/libgenometools.a endif Modified: trunk/packages/genometools/trunk/debian/patches/libbam-fix === --- trunk/packages/genometools/trunk/debian/patches/libbam-fix 2013-02-05 09:23:24 UTC (rev 12913) +++ trunk/packages/genometools/trunk/debian/patches/libbam-fix 2013-02-05 18:13:50 UTC (rev 12914) @@ -1,6 +1,6 @@ --- a/Makefile +++ b/Makefile -@@ -240,7 +240,7 @@ +@@ -251,7 +251,7 @@ # add necessary shared lib dependencies then not building them ourselves ifeq ($(useshared),yes) DEPLIBS:=-lm -lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \ @@ -9,7 +9,7 @@ else DEPLIBS:= endif -@@ -576,6 +576,10 @@ +@@ -591,6 +591,10 @@ @$(RANLIB) $@ endif @@ -20,7 +20,7 @@ lib/libgenometools.a: obj/gt_config.h $(LIBGENOMETOOLS_OBJ) @echo "[link $(@F)]" @test -d $(@D) || mkdir -p $(@D) -@@ -593,12 +597,13 @@ +@@ -608,12 +612,13 @@ lib/libgenometools$(SHARED_OBJ_NAME_EXT): obj/gt_config.h \ $(LIBGENOMETOOLS_OBJ) \ $(ADDITIONAL_SO_DEPS) \ @@ -36,7 +36,7 @@ lib/libtecla.a: $(LIBTECLA_OBJ) @echo "[link $(@F)]" -@@ -619,51 +624,61 @@ +@@ -634,51 +639,61 @@ $(eval $(call PROGRAM_template, bin/skproto, $(SKPROTO_OBJ) \ lib/libgenometools.a \ ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
