[med-svn] [snp-sites] annotated tag debian/2.3.3-2 created (now 93a64ee)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag debian/2.3.3-2 in repository snp-sites. at 93a64ee (tag) tagging 8d96dcc578d00d80560475eb8b3b0e75e0cccd73 (commit) replaces debian/2.3.2-1 tagged by Sascha Steinbiss on Sun Jun 18 17:36:44 2017 + - Log - snp-sites Debian release 2.3.3-2 -BEGIN PGP SIGNATURE- iQIzBAABCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAllGuiwACgkQ6NN64vCf SHKGjhAAj0fChsiYh/KZPgkYva7I13dBX1CSN47wP8xOhw4RRGzJH3DBt3VSejSG dlJjextfFPSXL8nJIMJ2Mq+Y81DUlWZLT80a5EL5Xvd/j4U5qx/6TR9mhawz2JjZ pmYGfBU/9vxwPOhwiw+VPy9zbjZwYD8DtuGrZJUK8+LN8nBRk1PGU1Ppp5nzFDME jUwH6dPjKj65EkIwPe+jgau8W42aMwbFSKL0gXEpZLPy0KqF6SMTeyUbfgoJXLuR HrulRp/W8tQyDqe9K/fZ4YFP2F86OzbxyXALgvMgLovAInD4bOzB8bKVZgX57oBz +4TcPLOTR65Vke3Nm/CctL/wUApZEp7GxCvE7XyW9Zih9oM+/SzBrXZuvEOFXrq4 DmBxSeS33DrzbCWGp0dD9w6AUyICD1iR1Ecl/Iec1MNsX+wapzvdthpwZ1nqE7qe ZPLCQ6s73QKj4dg2N8CqFiar66jtgTcERJBLiRjo5NaEzRs9P8Mi848jugocDwPf iYEOgd30gIT8tk8O4EfpzThfbd1YdmKU2Na6qyImSDdOJcAzxldJzT1guDvIK8xK rr30nidqjn6u8v+H00l1B8v47b6ezeqn52e6EKtlT//B+oz56X16/ELT4JP++D4A pffTkV5GuNoUzR8MNguU57WtbFx0c6sEsvAORvjKLqNS7jEg8JY= =/LKN -END PGP SIGNATURE- Sascha Steinbiss (5): New upstream version 2.3.3 Merge tag 'upstream/2.3.3' new upstream version update email address upload to unstable Steffen Moeller (1): Corrected EDAM annotation file --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snp-sites.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] 04/04: upload to unstable
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository fastaq. commit bc79b54768e305f097c06cf0de95118af0690e86 Author: Sascha Steinbiss <sa...@debian.org> Date: Sun Jun 18 17:22:28 2017 + upload to unstable --- debian/changelog | 6 ++ 1 file changed, 6 insertions(+) diff --git a/debian/changelog b/debian/changelog index 38505a6..731f043 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +fastaq (3.15.0-2) unstable; urgency=medium + + * Upload to unstable. + + -- Sascha Steinbiss <sa...@debian.org> Sun, 18 Jun 2017 17:22:15 + + fastaq (3.15.0-1) experimental; urgency=medium * New upstream release. -- 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] 01/04: Revert "Revert "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 552f25468145f7ed645801a63fff31fca14731a5 Author: Sascha Steinbiss <sa...@debian.org> Date: Sun Jun 18 17:21:29 2017 + Revert "Revert "new upstream release"" This reverts commit 4c793d761670150ef01aaff4697a4753f79face4. --- debian/changelog | 6 ++ 1 file changed, 6 insertions(+) diff --git a/debian/changelog b/debian/changelog index 0fbd12d..5438e62 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +fastaq (3.15.0-1) experimental; urgency=medium + + * New upstream release. + + -- Sascha Steinbiss <sa...@debian.org> Mon, 20 Feb 2017 12:27:52 +0100 + fastaq (3.14.0-1) unstable; urgency=medium * New upstream release. -- 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 experimental deleted (was e87202d)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch experimental in repository fastaq. was e87202d drop patches applied by upstream The revisions that were on this branch are still contained in other references; therefore, this change does not discard any commits from the repository. -- 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/3.15.0-2 created (now 5e7c9e8)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag debian/3.15.0-2 in repository fastaq. at 5e7c9e8 (tag) tagging bc79b54768e305f097c06cf0de95118af0690e86 (commit) replaces debian/3.14.0-1 tagged by Sascha Steinbiss on Sun Jun 18 17:31:15 2017 + - Log - fastaq Debian release 3.15.0-2 -BEGIN PGP SIGNATURE- iQIzBAABCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAllGuOMACgkQ6NN64vCf SHJm9w/9GMaUxwVUKVAD2oBjbembLscnea0TrEDNNXjOo0J7oGF7kOvUu+ZZ4ocz Ukkh0Mm5HfzQKVFf3NGyw1rQuRNewqf8alN7pPprfNlt+ytC1+3jJ/3mGDBeKjIV i/n49/CsuiGKjFTZ2N0Cyo4/0Dm9vFG2AGN7PeQr+HzqMnQzoYvYFLWInqJFlYAS XeF0EpI8RDmq9zETN9REmxVQ5qgJrhTGrEbWtp8e1jyqu6Q65MFS9LR6Up+s7SB/ Gvhs9jNfIqNBOnWxH5CL1Wqi91VXcDa9OuG+yk6o5vY+6D8FQSbys5Q0doRiEIbA blU5jm05EEI4qc4LLvnhiVNN4NJPsvJrZ/SONEu0ZCbWs0m/hYlqQA/VD89OVAVV mnrUmfrVdQtc7H99SsSJotki7/lU+hfJjvj5Xm3UPAnoG3PCKs/EX4ksE+Rxv5Ml dm4xXzKsg3KKShJ20nfr7FsPo2T/eehDl1WMpAWXDNhYdtPsUjxUU1+mS7GQAxco FVcNypP/I8SYuoi17vH/yx9alt7Pew5zc289WqsARYiNOBn9tDcFBdadjb45+ytX pu+rsBCADm0ngfgZvAoQEn+IUJQBNSg7+dQie3Jg7dFE83mtVLOrzXo8OJI0MefH qKJPzpXV9Og4kMLbpRyVOZhn/XXBKRGoYpl0P9oxgIHSUB8G2uw= =kKgA -END PGP SIGNATURE- Sascha Steinbiss (11): new upstream release New upstream version 3.15.0 Merge tag 'upstream/3.15.0' drop patches applied by upstream Revert "drop patches applied by upstream" Revert "Merge tag 'upstream/3.15.0'" Revert "new upstream release" Revert "Revert "new upstream release"" Revert "Revert "Merge tag 'upstream/3.15.0'"" Revert "Revert "drop patches applied by upstream"" upload to unstable Steffen Moeller (2): Corrected EDAM annotation file Corrected EDAM annotation file --- 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] 02/04: Revert "Revert "Merge tag 'upstream/3.15.0'""
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository fastaq.
commit 11f33d4fe0209ef719ed2e95748b130362a517df
Author: Sascha Steinbiss <sa...@debian.org>
Date: Sun Jun 18 17:21:40 2017 +
Revert "Revert "Merge tag 'upstream/3.15.0'""
This reverts commit fbcbefdb8d1c46dc72186a52466ecc15216dd975.
---
README.md | 1 +
pyfastaq/runners/make_random_contigs.py| 2 +-
pyfastaq/runners/sort_by_name.py | 14 ++
pyfastaq/tasks.py | 12
pyfastaq/tests/data/tasks_test_sort_by_name.in.fa | 16
pyfastaq/tests/data/tasks_test_sort_by_name.out.fa | 16
pyfastaq/tests/tasks_test.py | 9 +
scripts/fastaq | 3 ++-
setup.py | 2 +-
9 files changed, 72 insertions(+), 3 deletions(-)
diff --git a/README.md b/README.md
index c17c54f..675cb2f 100644
--- a/README.md
+++ b/README.md
@@ -79,6 +79,7 @@ Available commands
| scaffolds_to_contigs | Creates a file of contigs from a file of scaffolds
|
| search_for_seq| Find all exact matches to a string (and its reverse
complement) |
| sequence_trim | Trim exact matches to a given string off the start
of every sequence |
+| sort_by_name | Sorts sequences in lexographical (name) order
|
| sort_by_size | Sorts sequences in length order
|
| split_by_base_count | Split multi sequence file into separate files
|
| strip_illumina_suffix | Strips /1 or /2 off the end of every read name
|
diff --git a/pyfastaq/runners/make_random_contigs.py
b/pyfastaq/runners/make_random_contigs.py
index 5337120..6b5febb 100644
--- a/pyfastaq/runners/make_random_contigs.py
+++ b/pyfastaq/runners/make_random_contigs.py
@@ -9,7 +9,7 @@ def run(description):
parser.add_argument('--name_by_letters', action='store_true', help='Name
the contigs A,B,C,... will start at A again if you get to Z')
parser.add_argument('--prefix', help='Prefix to add to start of every
sequence name', default='')
parser.add_argument('--seed', type=int, help='Seed for random number
generator. Default is to use python\'s default', default=None)
-parser.add_argument('contigs', type=int, help='Nunber of contigs to make')
+parser.add_argument('contigs', type=int, help='Number of contigs to make')
parser.add_argument('length', type=int, help='Length of each contig')
parser.add_argument('outfile', help='Name of output file')
options = parser.parse_args()
diff --git a/pyfastaq/runners/sort_by_name.py b/pyfastaq/runners/sort_by_name.py
new file mode 100644
index 000..f57911f
--- /dev/null
+++ b/pyfastaq/runners/sort_by_name.py
@@ -0,0 +1,14 @@
+import argparse
+from pyfastaq import tasks
+
+def run(description):
+parser = argparse.ArgumentParser(
+description = description,
+usage = 'fastaq sort_by_name ')
+parser.add_argument('infile', help='Name of input file')
+parser.add_argument('outfile', help='Name of output file')
+options = parser.parse_args()
+tasks.sort_by_name(
+options.infile,
+options.outfile
+)
diff --git a/pyfastaq/tasks.py b/pyfastaq/tasks.py
index 3107672..b788672 100644
--- a/pyfastaq/tasks.py
+++ b/pyfastaq/tasks.py
@@ -556,6 +556,18 @@ def sort_by_size(infile, outfile, smallest_first=False):
utils.close(fout)
+def sort_by_name(infile, outfile):
+'''Sorts input sequence file by sort -d -k1,1, writes sorted output
file.'''
+seqs = {}
+file_to_dict(infile, seqs)
+#seqs = list(seqs.values())
+#seqs.sort()
+fout = utils.open_file_write(outfile)
+for name in sorted(seqs):
+print(seqs[name], file=fout)
+utils.close(fout)
+
+
def to_fastg(infile, outfile, circular=None):
'''Writes a FASTG file in SPAdes format from input file. Currently only
whether or not a sequence is circular is supported. Put circular=set of ids, or
circular=filename to make those sequences circular in the output. Puts
coverage=1 on all contigs'''
if circular is None:
diff --git a/pyfastaq/tests/data/tasks_test_sort_by_name.in.fa
b/pyfastaq/tests/data/tasks_test_sort_by_name.in.fa
new file mode 100644
index 000..26c1d8f
--- /dev/null
+++ b/pyfastaq/tests/data/tasks_test_sort_by_name.in.fa
@@ -0,0 +1,16 @@
+>scaffold1
+AGTCA
+>scaffold2
+ACGTTT
+>scaffold10
+A
+>scaffold12
+ACG
+>contig1
+AGTCA
+>contig2
+ACGTTT
+>contig10
+A
+>contig12
+ACG
\ No newline at end of file
diff --git a/pyfastaq/tests/data/tasks_test_sort_by_name.out.fa
b/pyfastaq/tests/data/tasks_test_sort_by_name.out.fa
new file mode 100644
index 00
[med-svn] [fastaq] branch master updated (4c793d7 -> bc79b54)
This is an automated email from the git hooks/post-receive script.
satta pushed a change to branch master
in repository fastaq.
from 4c793d7 Revert "new upstream release"
new 552f254 Revert "Revert "new upstream release""
new 11f33d4 Revert "Revert "Merge tag 'upstream/3.15.0'""
new 73c1f66 Revert "Revert "drop patches applied by upstream""
new bc79b54 upload to unstable
The 4 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:
README.md| 1 +
debian/changelog | 13 +
debian/patches/series| 1 -
pyfastaq/runners/make_random_contigs.py | 2 +-
.../{strip_illumina_suffix.py => sort_by_name.py}| 7 +--
pyfastaq/tasks.py| 12
pyfastaq/tests/data/tasks_test_sort_by_name.in.fa| 16
pyfastaq/tests/data/tasks_test_sort_by_name.out.fa | 16
pyfastaq/tests/tasks_test.py | 9 +
scripts/fastaq | 3 ++-
setup.py | 2 +-
11 files changed, 76 insertions(+), 6 deletions(-)
copy pyfastaq/runners/{strip_illumina_suffix.py => sort_by_name.py} (68%)
create mode 100644 pyfastaq/tests/data/tasks_test_sort_by_name.in.fa
create mode 100644 pyfastaq/tests/data/tasks_test_sort_by_name.out.fa
--
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[med-svn] [libtabixpp] annotated tag debian/1.0.0-3 created (now dc4a8d5)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag debian/1.0.0-3 in repository libtabixpp. at dc4a8d5 (tag) tagging d22829b729702a23cf122adf1224353ad65bb6ed (commit) replaces debian/1.0.0-2 tagged by Sascha Steinbiss on Sun Jun 18 17:17:59 2017 + - Log - libtabixpp Debian release 1.0.0-3 -BEGIN PGP SIGNATURE- iQIzBAABCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAllGtccACgkQ6NN64vCf SHLIOA//W2Bshnv2VaPYD6lQR65x3ofunwoCZMxzYemfKGBhdku8dtDGB7ZWCdt1 caSBN67BxmGsR0h6tV8/d4v7MHM+r7V2E0gp+0Nev94cKnt3TlKEdc3/T9msjHTc 69dJUM5wzZBe5hwrgPa2B/vbkJCTmqVbZTR9SiAyipFhz6+9tiFXtkRT4d9gc4xR Wx1wi5EpLMdp/CI+70x8HiFuLd26Xlqm3gFOE4M73fEXf7HafGCbWvk+RkQ1NWAV DnQ1BRE2zYIRE3a+7phIO/17hx/EG4X7Ps1VsoqZRW1hLvJF5fjuc1iQJPgXWxl+ rvhLXfHZRsnKhkwm0Qo/qeh/PIz061RA/L3FIFtMuZuQLxs6baOPWOTQBoqsE3R9 /a7SN5Vfp8u2F2R92dxqzkuyk9yM0vaQVdm3U+Hbz4CWNM6Q2nRbL7CslKwlI++e sXLgrcRX03+fjEWlHbwjZLHjcy4mbjVhFYXk3QMuHuxL2yRkCGM7in7mrfJ6/2d/ 5s8hJwJXSFMn62JXTChItPQ5ZF5lRmXGyXyltDs3kA10OJZl2S38OI13E2yPcQ1L 1K+lB2NaJcSlb4I/IiPdYvr+5MUJg5wTw4DZpc1DwqsFUpSci0lhnEzIS9XsmcBJ 49/mocx345EIR3s7kSuG3oWlSBn3Ddtph8qt2MiAVX4Q2CWWDHA= =Fns/ -END PGP SIGNATURE- Sascha Steinbiss (5): fix FTBFS update uploader email address bump Standards-Version use secure Vcs-Git enable full hardening --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libtabixpp.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] [libtabixpp] 05/05: enable full hardening
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository libtabixpp. commit d22829b729702a23cf122adf1224353ad65bb6ed Author: Sascha Steinbiss <sa...@debian.org> Date: Sun Jun 18 17:12:24 2017 + enable full hardening --- debian/changelog | 1 + debian/rules | 1 + 2 files changed, 2 insertions(+) diff --git a/debian/changelog b/debian/changelog index a6195ac..3c11bb8 100644 --- a/debian/changelog +++ b/debian/changelog @@ -5,6 +5,7 @@ libtabixpp (1.0.0-3) unstable; urgency=medium * Update uploader email address. * Bump Standards-Version. * Use secure Vcs-Git. + * Enable full hardening. -- Sascha Steinbiss <sa...@debian.org> Sun, 18 Jun 2017 17:06:51 + diff --git a/debian/rules b/debian/rules index 625d2e9..7c8cd7d 100755 --- a/debian/rules +++ b/debian/rules @@ -1,6 +1,7 @@ #!/usr/bin/make -f # DH_VERBOSE := 1 +export DEB_BUILD_MAINT_OPTIONS = hardening=+all DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH) %: -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libtabixpp.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] [libtabixpp] 04/05: use secure Vcs-Git
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository libtabixpp. commit 6752f00df0f761203bb42f25b1f6679139ae6b4f Author: Sascha Steinbiss <sa...@debian.org> Date: Sun Jun 18 17:11:02 2017 + use secure Vcs-Git --- debian/changelog | 1 + debian/control | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index f243ff5..a6195ac 100644 --- a/debian/changelog +++ b/debian/changelog @@ -4,6 +4,7 @@ libtabixpp (1.0.0-3) unstable; urgency=medium Closes: #865007 * Update uploader email address. * Bump Standards-Version. + * Use secure Vcs-Git. -- Sascha Steinbiss <sa...@debian.org> Sun, 18 Jun 2017 17:06:51 + diff --git a/debian/control b/debian/control index 568a881..89a511b 100644 --- a/debian/control +++ b/debian/control @@ -10,7 +10,7 @@ Build-Depends: debhelper (>= 9), d-shlibs Standards-Version: 3.9.8 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libtabixpp.git -Vcs-Git: git://anonscm.debian.org/debian-med/libtabixpp.git +Vcs-Git: https://anonscm.debian.org/git/debian-med/libtabixpp.git Homepage: https://github.com/ekg/tabixpp Package: libtabixpp0 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libtabixpp.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] [libtabixpp] branch master updated (3e96d15 -> d22829b)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch master in repository libtabixpp. from 3e96d15 move dependencies around new a3b8801 fix FTBFS new 3c9c195 update uploader email address new 34aec1e bump Standards-Version new 6752f00 use secure Vcs-Git new d22829b enable full hardening 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: debian/changelog | 11 +++ debian/control | 6 +++--- debian/rules | 3 ++- 3 files changed, 16 insertions(+), 4 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libtabixpp.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] [libtabixpp] 01/05: fix FTBFS
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository libtabixpp. commit a3b8801a713042b83507f4a50a47233d7311b453 Author: Sascha Steinbiss <sa...@debian.org> Date: Sun Jun 18 17:08:45 2017 + fix FTBFS --- debian/changelog | 7 +++ debian/rules | 2 +- 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index fe39de7..a6a3158 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +libtabixpp (1.0.0-3) unstable; urgency=medium + + * Fix FTBFS with htslib 1.4.1-2. +Closes: #865007 + + -- Sascha Steinbiss <sa...@debian.org> Sun, 18 Jun 2017 17:06:51 + + libtabixpp (1.0.0-2) unstable; urgency=medium * d/tests/control: depend on unversioned dev package diff --git a/debian/rules b/debian/rules index 6a756b8..625d2e9 100755 --- a/debian/rules +++ b/debian/rules @@ -11,7 +11,7 @@ override_dh_auto_install: d-shlibmove --commit \ --multiarch \ --devunversioned \ ---override s/libhts1-dev/libhts-dev/ \ +--override s/libhts2-dev/libhts-dev/ \ --movedev "*.hpp" usr/include/ \ libtabixpp.so -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libtabixpp.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] [libtabixpp] 02/05: update uploader email address
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository libtabixpp. commit 3c9c195811746391807687ebb549931dda8457d6 Author: Sascha Steinbiss <sa...@debian.org> Date: Sun Jun 18 17:09:02 2017 + update uploader email address --- debian/changelog | 1 + debian/control | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index a6a3158..32c2ea5 100644 --- a/debian/changelog +++ b/debian/changelog @@ -2,6 +2,7 @@ libtabixpp (1.0.0-3) unstable; urgency=medium * Fix FTBFS with htslib 1.4.1-2. Closes: #865007 + * Update uploader email address. -- Sascha Steinbiss <sa...@debian.org> Sun, 18 Jun 2017 17:06:51 + diff --git a/debian/control b/debian/control index 6df9e7b..58ceda6 100644 --- a/debian/control +++ b/debian/control @@ -3,7 +3,7 @@ Section: science Priority: optional Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Uploaders: Andreas Tille <ti...@debian.org>, - Sascha Steinbiss <sas...@steinbiss.name> + Sascha Steinbiss <sa...@debian.org> Build-Depends: debhelper (>= 9), libhts-dev, zlib1g-dev, -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libtabixpp.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] [libtabixpp] 03/05: bump Standards-Version
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository libtabixpp. commit 34aec1ec074f63428be7faa44ed78ed3dab80258 Author: Sascha Steinbiss <sa...@debian.org> Date: Sun Jun 18 17:09:11 2017 + 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 32c2ea5..f243ff5 100644 --- a/debian/changelog +++ b/debian/changelog @@ -3,6 +3,7 @@ libtabixpp (1.0.0-3) unstable; urgency=medium * Fix FTBFS with htslib 1.4.1-2. Closes: #865007 * Update uploader email address. + * Bump Standards-Version. -- Sascha Steinbiss <sa...@debian.org> Sun, 18 Jun 2017 17:06:51 + diff --git a/debian/control b/debian/control index 58ceda6..568a881 100644 --- a/debian/control +++ b/debian/control @@ -8,7 +8,7 @@ Build-Depends: debhelper (>= 9), libhts-dev, zlib1g-dev, d-shlibs -Standards-Version: 3.9.6 +Standards-Version: 3.9.8 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libtabixpp.git Vcs-Git: git://anonscm.debian.org/debian-med/libtabixpp.git Homepage: https://github.com/ekg/tabixpp -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libtabixpp.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] [spades] annotated tag upstream/3.10.0+dfsg created (now a11e228)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag upstream/3.10.0+dfsg in repository spades. at a11e228 (tag) tagging 55e89edffa500c8f0d1fdc423884571ac501e59b (commit) replaces upstream/3.9.1+dfsg tagged by Sascha Steinbiss on Sat Feb 25 14:00:07 2017 + - Log - Upstream version 3.10.0+dfsg Sascha Steinbiss (1): New upstream version 3.10.0+dfsg --- This annotated tag includes the following new commits: new 55e89ed New upstream version 3.10.0+dfsg 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. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.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] [spades] annotated tag debian/3.10.1+dfsg-2 created (now 03bb78e)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag debian/3.10.1+dfsg-2 in repository spades. at 03bb78e (tag) tagging bffd3b3784afccfaf7a064db8a5f1fefdbaecc80 (commit) replaces debian/3.9.1+dfsg-1 tagged by Sascha Steinbiss on Sun Jun 18 17:02:18 2017 + - Log - spades Debian release 3.10.1+dfsg-2 -BEGIN PGP SIGNATURE- iQIzBAABCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAllGshoACgkQ6NN64vCf SHLrVhAAjn4izpWLG4V3XMyQwANRGFc/BRklP45/x72GRpY6+iXybxKwZGAn+RW2 aV5/ZkF+7EAa1LKl0f2hovnrcQ1DYHq4cL2hMgK5o83GsYStbEutnS9ZWSfz6ceC 6FgYmAKLgoactpwdkGLOc3FNF1DTXyK4WNE3X/+fTRhIHTcan/fgrw3nt6Lt6iv/ HAYUqcx3Pg7sxP3wgwrg2rwQgF5Rkhkn0Wv0NLKjGgJIynsYL18/RIP5zVgCV+e5 YTPBmixH9MaIxsH8oS/cQyw4KvSovNLPnGHV483h2gFtlPm4V5yRVLVA8zznO9H2 NOlCJI7xA6zAHm8/gtk3dlJ1zyt9LTr3K1Zcf0pEEDyh31SpCpAINARlJXKbubi4 MD3aT7mWD26zKVwmZhZj7kA6RnbcY0C+CFQKb4ud1G9Zhz0LQMyh+vzkyTBMYju8 WXJnvJEsut1/ENgbYCwwcxxpyW2T1RpRFRikX/qEHGcAg1Hrxxueu0tUik++qdJA iVIAjvtizOP2QlQMlyVnmwr2Eiz9lBWNstL5igyYEeXCjGazEbiD39Miz3XxAqjC SOIgDpIuRESTCZEERjstd3j7kW5ubk/yXwAHdm6+bhHurc5Ox8N7O2MYZXKqLcms u1t5DExLJki5j6mX4zDdD20hdIgSpblW+K6Nf6V4mdlgGrIComM= =t5Lu -END PGP SIGNATURE- Michael R. Crusoe (5): update copyright for new release New upstream version 3.10.1+dfsg Merge tag 'upstream/3.10.1+dfsg' New upstream version 3.10.1 spelling fixes Sascha Steinbiss (2): build for experimental upload to unstable --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.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] [spades] 01/01: upload to unstable
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository spades. commit bffd3b3784afccfaf7a064db8a5f1fefdbaecc80 Author: Sascha Steinbiss <sa...@debian.org> Date: Sun Jun 18 16:32:20 2017 + upload to unstable --- debian/changelog | 6 ++ 1 file changed, 6 insertions(+) diff --git a/debian/changelog b/debian/changelog index f04ddad..bdbb740 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +spades (3.10.1+dfsg-2) unstable; urgency=medium + + * Upload to unstable. + + -- Sascha Steinbiss <sa...@debian.org> Sun, 18 Jun 2017 16:31:57 + + spades (3.10.1+dfsg-1) experimental; urgency=medium [ Michael R. Crusoe ] -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.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] [spades] branch master updated (87072be -> bffd3b3)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch master in repository spades. from 87072be spelling fixes adds 556fb32 build for experimental new bffd3b3 upload to unstable 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 | 14 -- 1 file changed, 12 insertions(+), 2 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.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] [roary] annotated tag debian/3.8.2+dfsg-2 created (now 4e1ad45)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag debian/3.8.2+dfsg-2 in repository roary. at 4e1ad45 (tag) tagging 16288ee9e65e35a01b8b86ad7320579dde32db04 (commit) replaces debian/3.8.0+dfsg-1 tagged by Sascha Steinbiss on Sun Jun 18 12:19:08 2017 + - Log - roary Debian release 3.8.2+dfsg-2 -BEGIN PGP SIGNATURE- iQIzBAABCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAllGb7wACgkQ6NN64vCf SHLYNA//eU8baUWkWdCbEHhME/vn2UTQnrnJErm83RsowQ3KHfHP0Zrb70Js8a78 xYc0Ec2d4ggV7mWUVtjX/jLoZJfSw39Z4NVm6JQD4Ji5aSAO1hkoPDCU28nloyNX iF4li0/hSK5Pa/NsO29Q4DKPxOLOpxOhSvCgFTf7He/SLn9bythaZV8yCrpvBmLK J0wtuwOhnATeeE/sF4u66SE5Fn4hZVG938+AXe+qswcekjAHCAR/KAFcD/bUlaOg zwikslFXdxA5IPxF6CpgIn0aXhii8GnszBmNXz6FRvnVcZSkoH5ENm/sYIVQxOit WtTi7jVMrHB1joOAMfazRtmKtmlFIWQZRa5ikddo24v7DMH9WB9vJi6z0n+hTn7o TkyeZLBzOb8jObDCRj8AXaMR0Q95TkhqXTOwZOuovD+KrwGM6wTpxyt+SlxyeK2d V3ndimUk2LAlw5rFIVKP1SudAkmC5yaKWFkSCCa5EFChEO4u7mXezZtfiiwE/xO4 6G75aDt1FsRn09BXpuA5qHSEpgfNOiMc/GDrZVthHws6VI4ONyuOo1hx1BEO+Fj7 2kFXVjC9yh/eWJLv5GPeRZoS4/Rhp9+5wES9x7CJz9XW525LqugPd/qOKam51UsL xAQesrivqJ9FJ1OgzqZoHDvqOEmg1GIsgpCCn6EnDbxc5apC/IY= =kTJe -END PGP SIGNATURE- Sascha Steinbiss (4): New upstream version 3.8.2+dfsg Merge tag 'upstream/3.8.2+dfsg' into experimental new upstream release upload to unstable --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/roary.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] [roary] branch master updated (08f9fa3 -> 16288ee)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch master in repository roary. from 08f9fa3 new upstream release adds c94f09a New upstream version 3.8.2+dfsg adds 07e2034 Merge tag 'upstream/3.8.2+dfsg' into experimental adds 71ed165 new upstream release new 16288ee upload to unstable 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 +- README.md | 26 +- debian/changelog | 12 dist.ini | 2 +- lib/Bio/Roary.pm | 2 ++ lib/Bio/Roary/CommandLine/Roary.pm | 8 +++- lib/Bio/Roary/External/Mcl.pm | 4 ++-- 7 files changed, 38 insertions(+), 18 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/roary.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] [roary] 01/01: upload to unstable
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository roary. commit 16288ee9e65e35a01b8b86ad7320579dde32db04 Author: Sascha Steinbiss <sa...@debian.org> Date: Sun Jun 18 12:19:00 2017 + upload to unstable --- debian/changelog | 6 ++ 1 file changed, 6 insertions(+) diff --git a/debian/changelog b/debian/changelog index fca04c4..5072206 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +roary (3.8.2+dfsg-2) unstable; urgency=medium + + * Upload to unstable. + + -- Sascha Steinbiss <sa...@debian.org> Sun, 18 Jun 2017 12:00:16 + + roary (3.8.2+dfsg-1) experimental; urgency=medium * New upstream release. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/roary.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] [libhat-trie] branch master updated (9b99425 -> 0d44006)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch master in repository libhat-trie. from 9b99425 Override can be removed in d-shlibs (>= 0.79) [I noticed that d-shlibs is not used at all but I try to avoid false positives when seeking for unused overrides] adds 3c6fb6e New upstream version 0.1.1 adds 455bff8 Merge tag 'upstream/0.1.1' into experimental adds 08efea9 new upstream release adds f76bda5 refresh patches new 2c76ab2 Merge branch 'experimental' new 0d44006 upload to unstable The 2 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: configure.ac | 4 +- debian/changelog | 13 + debian/copyright | 7 +++ debian/patches/reproducible.patch | 4 +- src/ahtable.c | 83 +++ src/ahtable.h | 4 ++ src/hat-trie.h| 1 - src/portable_endian.h | 116 ++ test/check_ahtable.c | 51 + 9 files changed, 278 insertions(+), 5 deletions(-) create mode 100644 src/portable_endian.h -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libhat-trie.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] [libhat-trie] 01/02: Merge branch 'experimental'
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository libhat-trie. commit 2c76ab21e1801fb962d5461c39675273f633f7f3 Merge: 9b99425 f76bda5 Author: Sascha Steinbiss <sa...@debian.org> Date: Sun Jun 18 11:27:48 2017 + Merge branch 'experimental' configure.ac | 4 +- debian/changelog | 7 +++ debian/copyright | 7 +++ debian/patches/reproducible.patch | 4 +- src/ahtable.c | 83 +++ src/ahtable.h | 4 ++ src/hat-trie.h| 1 - src/portable_endian.h | 116 ++ test/check_ahtable.c | 51 + 9 files changed, 272 insertions(+), 5 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libhat-trie.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] [libhat-trie] 02/02: upload to unstable
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository libhat-trie. commit 0d4400688fc1bbaf5d8cfad37b7991cf60efefb3 Author: Sascha Steinbiss <sa...@debian.org> Date: Sun Jun 18 11:28:55 2017 + upload to unstable --- debian/changelog | 6 ++ 1 file changed, 6 insertions(+) diff --git a/debian/changelog b/debian/changelog index f3e3fd8..3f65c24 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +libhat-trie (0.1.1-2) unstable; urgency=medium + + * Upload to unstable. + + -- Sascha Steinbiss <sa...@debian.org> Sun, 18 Jun 2017 11:27:56 + + libhat-trie (0.1.1-1) experimental; urgency=medium * New versioned upstream release. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libhat-trie.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] [libhat-trie] annotated tag debian/0.1.1-2 created (now 774e8b8)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag debian/0.1.1-2 in repository libhat-trie. at 774e8b8 (tag) tagging 0d4400688fc1bbaf5d8cfad37b7991cf60efefb3 (commit) replaces debian/0.0_git25f9e946-2 tagged by Sascha Steinbiss on Sun Jun 18 11:40:56 2017 + - Log - libhat-trie Debian release 0.1.1-2 -BEGIN PGP SIGNATURE- iQIzBAABCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAllGZsgACgkQ6NN64vCf SHJhSA//UynWRKZFVaMBkn2/5x281Lebv/Clls0GT0y6dH62SuEcfgVkotyL26Vo Uny27R2KS72w1X+yFyMK/8BU3Boam+PLIknnYJ9ZkqDIDTR9r6ZHqnvx9Ic8sMq4 QK1w/E5qABeW8iNvWWdU8P++W+hI2hvgAxd6BXt7WFW7e9CsccoRVhzCOB/L4QnG 0HSM6dNmrXvg/Z0D8wDY3q3PImZmv26fJSMkyEqyk0wPthgV7Vi0YQrvl28wua0D vNDH+TdIsMOhbCzJMLHOvfNcXCL93N+P3AryiE2S1KPPq5UK0ZmY23gScLkZcupP X/i6MQt2KnAQNIYijUxear8QBKZmi5eTttD5+OGhIyGosUmmfmkpKCaSq21EmpYF vcZuyNva08IYZoQqIqW8lxs0Il7rX8imjMub42qn/FqvFmqmMl8E7DqwBUnxXxgD nCVKb3zClYOiVyw7FvlUZWVu0IFN7Y7CNYXtvCd7z6NOLp2gDCss8enCLV12Cmd0 cmmH2BpbnZPAZIl18k+ktvTYstD5ItkkaXpgs9LR46XKL/rQH6j/hjRi3ewLOTT+ M+OXiFN7/lNTqfxRTvuzcvrIFBzphPyqHJ2URwGIINAssM9m1XtYVPFOUvNO5rSp n7MMSrxsYigNshVP9bRdDbXsCbWkLJJ/winuszHTUVDnr0zqylI= =0G+a -END PGP SIGNATURE- Andreas Tille (1): Override can be removed in d-shlibs (>= 0.79) [I noticed that d-shlibs is not used at all but I try to avoid false positives when seeking for unused overrides] Sascha Steinbiss (6): New upstream version 0.1.1 Merge tag 'upstream/0.1.1' into experimental new upstream release refresh patches Merge branch 'experimental' upload to unstable --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libhat-trie.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/2.9.4+ds-2 created (now 6c77ecf)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag debian/2.9.4+ds-2 in repository ariba. at 6c77ecf (tag) tagging 20ef99a4873d7b68a7be6af8782de324f8c4196d (commit) replaces upstream/2.9.4+ds tagged by Sascha Steinbiss on Sun Jun 18 10:46:06 2017 + - Log - ariba Debian release 2.9.4+ds-2 -BEGIN PGP SIGNATURE- iQIzBAABCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAllGWe4ACgkQ6NN64vCf SHLxQQ//ZNKHy4xHRVaGwCdKHTRs3YoaqzWUlSlHhjjUjGtigv5WsDHV8XYZ0G7M wFBA+MbMlAofpTa/8roFGsBGa8me2eH3JUIcX6brzkBGEj4NbEwBAyEw4tc0jZ8B 5gF0bHn7qZcG/C2KHzKQNBNAQPENCLEO0K/YtqPWvF7661A9PGGFyRKPBtHiHZoV WMHrdZw5AblSpioXTCdm8IHLT3F+aFyWB/rvY2aoxGYDumJz3ZQRHdRFWk9rtDr1 Y1mSeUB4rSD2aaGimn/MWs98tgClrkliBG578ZTpHXcO5P/NTT5PtUVkWvbKElWZ anCgntP9JJDoZPxcSh7aRmiXwwBBGOOvsYtgrb3vZN7Y7RaDzoeC56KUIzFxR+L4 22MamxtWikdqWDg7zvSbXu3ykZiphtvhKVLjt5bVnCFIIkMhPvBmVReXnsvIuUh3 XFTZa0C2/DSVwelRh2AdlO9Gfj+6UvdtfAuZ/bnczIR4s5/WKaQThipNlsUI9yzu nSAKsk568kiynVD2qTldR2A/A4xvHDrbNBWUfRXnnA9zHvYV81ZRkzRrCj3Yqx2k E+4SMm3oCtHEqtxSDo//tpl/1MzKvFPoUleHb1/rBuOWcDJvebvt+ToQPoFBAcHf 27q4MYExA7VDw2Ydo8hhAdNcLTZ4f7MgS69Hz8an0WbzK72Sfq8= =iCkg -END PGP SIGNATURE- Andreas Tille (3): Adapt to fermi-lite which does not conflict with bwa Versioned depends to fixed libfml-dev, upload to experimental Realise that 2.7.2+ds-1 was not yet uploaded - fix changelog and re-upload to experimental Sascha Steinbiss (94): add debian dir flesh out first package add manpages fix spelling fix runtime depends remove unavailable tests, adjust binary names cme fix dpkg add README with time delay make velvet the default assembler use patch cme fix dpkg add nose tests adjust deps bump version to 1.0.0 Merge tag 'upstream/1.0.0' drop patches for old version get packaging up to speed adjust man page building relax pysam version for tests complete manpage building add autopkgtest cme fix dpkg clarify license and contact add ITP bug# adjust copyright years Merge tag 'upstream/1.0.1' bump Debian version update email address repack source tarball to exclude embedded code Merge tag 'upstream/2.0.0+ds' new Debian version, dependencies adjust patches update d/changelog use Debian packaged libraries for extension building use correct Debian version we now build a native extension adjust dependencies add patch header add bindnow hardening patch some upstream issues complete d/changelog use zip from GitHub Merge tag 'upstream/2.1.0+ds' drop patches addressed upstream in 2.1.0 simplify manpage building use more explicit version requirements Merge tag 'upstream/2.2.0+ds' bump Debian version Merge tag 'upstream/2.2.1+ds' Debian version bump Merge tag 'upstream/2.2.2+ds' Debian version bump Merge tag 'upstream/2.2.3+ds' Debian version bump Merge tag 'upstream/2.2.4+ds' Debian version bump Merge tag 'upstream/2.2.5+ds' remove deps on samtools and bcftools refresh patches Debian version bump fix Debian version Merge tag 'upstream/2.3.0+ds' bump Debian version Merge tag 'upstream/2.4.0+ds' remove obsolete patch Debian version bump Updated version 2.5.0+ds from 'upstream/2.5.0+ds' Debian version bump Updated version 2.5.1+ds from 'upstream/2.5.1+ds' new Debian version Merge tag 'upstream/2.6.0+ds' new Debian version Merge tag 'upstream/2.6.1+ds' new Debian version new upstream version Merge tag 'upstream/2.7.0+ds' Merge tag 'upstream/2.7.1+ds' new upstream release Merge tag 'upstream/2.7.2+ds' new upstream release raise pymummer version requirement fix pysam version requirement Merge tag 'upstream/2.9.0+ds' new upstream release Merge tag 'upstream/2.9.0+ds' into experimental add dependencies Merge tag 'upstream/2.9.2+ds' into experimental new upstream release target experimental Merge tag 'upstream/2.9.3+ds' into experimental new upstream version Merge tag 'upstream/2.9.4+ds' into experimental new upstream release upload to unstable --- 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 (8d2b3e7 -> 20ef99a)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch master in repository ariba. from 8d2b3e7 Merge tag 'upstream/2.9.0+ds' adds 1aed5c7 new upstream release adds b69312e New upstream version 2.9.0+ds adds b158677 Merge tag 'upstream/2.9.0+ds' into experimental adds 9ae9d47 add dependencies adds a3fddfd New upstream version 2.9.2+ds adds 606d1e4 Merge tag 'upstream/2.9.2+ds' into experimental adds 9ed80ce new upstream release adds 1e966f2 target experimental adds db1f8f0 New upstream version 2.9.3+ds adds 6ca3cc2 New upstream version 2.9.3+ds adds 7364eee Merge tag 'upstream/2.9.3+ds' into experimental adds 3817a8f new upstream version adds 3ba4058 New upstream version 2.9.4+ds adds 257b46b Merge tag 'upstream/2.9.4+ds' into experimental adds 1f9b8f4 new upstream release new 20ef99a upload to unstable 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 README.md| 22 +- ariba/assembly.py| 1 + ariba/card_record.py | 9 - ariba/cluster.py | 1 + ariba/clusters.py| 2 -- ariba/external_progs.py | 7 +++ ariba/mapping.py | 4 ariba/pubmlst_getter.py | 10 +- ariba/summary.py | 1 + ariba/tests/card_record_test.py | 3 +++ ariba/tests/data/pubmlst_rename_seqs.expected.fa | 10 ++ ariba/tests/data/pubmlst_rename_seqs.in.fa | 10 ++ ariba/tests/mapping_test.py | 3 +++ debian/changelog | 24 debian/control | 4 install_dependencies.sh | 10 +- setup.py | 2 +- 19 files changed, 109 insertions(+), 20 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: upload to unstable
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository ariba. commit 20ef99a4873d7b68a7be6af8782de324f8c4196d Author: Sascha Steinbiss <sa...@debian.org> Date: Sun Jun 18 10:45:50 2017 + upload to unstable --- debian/changelog | 6 ++ 1 file changed, 6 insertions(+) diff --git a/debian/changelog b/debian/changelog index aad7043..b61004e 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +ariba (2.9.4+ds-2) unstable; urgency=medium + + * Upload to unstable. + + -- Sascha Steinbiss <sa...@debian.org> Sun, 18 Jun 2017 10:30:10 + + ariba (2.9.4+ds-1) experimental; urgency=medium * New upstream version. -- 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] [barrnap] 01/01: upload to unstable
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository barrnap. commit 99cf60b29b3663496b755703fa9a4cdcf3fa100d Author: Sascha Steinbiss <sa...@debian.org> Date: Sun Jun 18 10:52:41 2017 + upload to unstable --- debian/changelog | 6 ++ 1 file changed, 6 insertions(+) diff --git a/debian/changelog b/debian/changelog index 0bd81b4..986c253 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +barrnap (0.8+dfsg-2) unstable; urgency=medium + + * Upload to unstable. + + -- Sascha Steinbiss <sa...@debian.org> Sun, 18 Jun 2017 10:34:08 + + barrnap (0.8+dfsg-1) experimental; urgency=medium * New upstream release. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/barrnap.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] [barrnap] annotated tag debian/0.8+dfsg-2 created (now 84403d9)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag debian/0.8+dfsg-2 in repository barrnap. at 84403d9 (tag) tagging 99cf60b29b3663496b755703fa9a4cdcf3fa100d (commit) replaces debian/0.7+dfsg-2 tagged by Sascha Steinbiss on Sun Jun 18 10:52:52 2017 + - Log - barrnap Debian release 0.8+dfsg-2 -BEGIN PGP SIGNATURE- iQIzBAABCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAllGW4QACgkQ6NN64vCf SHLTDxAAntZp0AGqiaDyhF5P9XyjNi9vxXG2eiIiKEF+0HdlgJm6jjvE/t4vxz2Z r0FgBovEPbcc020IfEiO/B7LFfE7cEAALVkol1a4xfOIqUjArPdWTjXzM+k9SSLW l294S2an7T7IqkWfRaA+bi3Huzrns9u6ixmOq44AeLKlNwGC4GRa13AnGzGRZgLL FPB+MHwYzIypnff2GGRFzG0YXxmqcu5YHJW3TD7oCeGY4jReo8myr0LaayX82MPq Gu8hnujiG3cKURgTP/aZO7hfG6OMbocf96+Xss5aRgZ5WahSadiyUxeDNzE7bGvX a+/wWhJcB+HLxfTrNIKNb0U1nTEG1OzShmxXX4txHu6hfWTTX13MFRjIr+cVujum 6b5VgiVMSERt4I5MdHCBmgMcnHzHb+iWPhzTf08T89iSDlVpJSaV0I9y+uj3KTky sp/QOyjwOY1uATI8HpRZj2fEdg1Qp1A5PMgI/1sCq/oZWmAeAMBUi2ME6GuMNrTx b6Zb47rv/NMZ852BJ1tGncJ+FLc9/hS3pNA+mRg13qmmVmEOzeya0n30mJ0YlTKX DIUZqc58bBbMWUQuM1j+1KrENi1ocCX1VGTkkBLhZIRKaau0bLeMS4yrZHA7thoU N8nRN8FwhGeu3TXNWedk3Cw4mEMu7aFx4RpWytuaz24MslOFzhs= =uPDc -END PGP SIGNATURE- Sascha Steinbiss (9): New upstream version 0.8 Merge tag 'upstream/0.8' new upstream version New upstream version 0.8+dfsg Merge tag 'upstream/0.8+dfsg' refresh patch Merge branch 'master' of ssh://git.debian.org/git/debian-med/barrnap bump Standards-Version upload to unstable Steffen Moeller (1): Corrected EDAM annotation file --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/barrnap.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] [barrnap] branch master updated (67cd052 -> 99cf60b)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch master in repository barrnap. from 67cd052 Corrected EDAM annotation file adds cb478cc New upstream version 0.8 adds 5ed942d Merge tag 'upstream/0.8' adds 1d17ab1 new upstream version adds f1e4e6f New upstream version 0.8+dfsg adds 9572f35 Merge tag 'upstream/0.8+dfsg' adds a4b6f54 refresh patch adds b05a5fe Merge branch 'master' of ssh://git.debian.org/git/debian-med/barrnap adds d453a3a bump Standards-Version new 99cf60b upload to unstable 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: bin/barrnap|14 +- db/arc.hmm | 7102 +-- db/bac.hmm | 7080 +-- db/euk.hmm | 6692 ++ db/mito.hmm| 14278 ++- debian/changelog |14 + debian/control | 4 +- debian/patches/use_debian_dirs |14 +- 8 files changed, 14145 insertions(+), 21053 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/barrnap.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] [snp-sites] 02/04: Merge tag 'upstream/2.3.3'
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository snp-sites. commit 4468d656f9a9017824fe21ec5c9016b7efe74a9d Merge: 5187860 298cfae Author: Sascha Steinbiss <sa...@debian.org> Date: Tue Jun 13 12:09:50 2017 +0200 Merge tag 'upstream/2.3.3' Upstream version 2.3.3 AUTHORS | 2 +- Dockerfile | 19 +++ LICENSE | 4 VERSION | 2 +- src/alignment-file.c | 2 +- src/snp-sites.c | 14 -- 6 files changed, 34 insertions(+), 9 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snp-sites.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] [snp-sites] 01/01: pristine-tar data for snp-sites_2.3.3.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 snp-sites. commit 47b6793e1f4dbd2793e43d88497310fd6ac83a2e Author: Sascha Steinbiss <sa...@debian.org> Date: Tue Jun 13 12:09:50 2017 +0200 pristine-tar data for snp-sites_2.3.3.orig.tar.gz --- snp-sites_2.3.3.orig.tar.gz.delta | Bin 0 -> 3414 bytes snp-sites_2.3.3.orig.tar.gz.id| 1 + 2 files changed, 1 insertion(+) diff --git a/snp-sites_2.3.3.orig.tar.gz.delta b/snp-sites_2.3.3.orig.tar.gz.delta new file mode 100644 index 000..b8ddca8 Binary files /dev/null and b/snp-sites_2.3.3.orig.tar.gz.delta differ diff --git a/snp-sites_2.3.3.orig.tar.gz.id b/snp-sites_2.3.3.orig.tar.gz.id new file mode 100644 index 000..375b573 --- /dev/null +++ b/snp-sites_2.3.3.orig.tar.gz.id @@ -0,0 +1 @@ +219645f55590a4689b68db3fb72ce50b188da805 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snp-sites.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] [snp-sites] branch upstream updated (6957554 -> 298cfae)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch upstream in repository snp-sites. from 6957554 Imported Upstream version 2.3.2 new 298cfae New upstream version 2.3.3 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 +- Dockerfile | 19 +++ LICENSE | 4 VERSION | 2 +- src/alignment-file.c | 2 +- src/snp-sites.c | 14 -- 6 files changed, 34 insertions(+), 9 deletions(-) create mode 100644 Dockerfile -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snp-sites.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] [snp-sites] branch master updated (5187860 -> be0a45f)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch master in repository snp-sites. from 5187860 Corrected EDAM annotation file new 298cfae New upstream version 2.3.3 new 4468d65 Merge tag 'upstream/2.3.3' new 22fea13 new upstream version new be0a45f update email address The 4 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 +- Dockerfile | 19 +++ LICENSE | 4 VERSION | 2 +- debian/changelog | 7 +++ debian/control | 2 +- src/alignment-file.c | 2 +- src/snp-sites.c | 14 -- 8 files changed, 42 insertions(+), 10 deletions(-) create mode 100644 Dockerfile -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snp-sites.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] [snp-sites] 04/04: update email address
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository snp-sites. commit be0a45f255a80643061a1e5e2ed3ca4eaff1e7b7 Author: Sascha Steinbiss <sa...@debian.org> Date: Tue Jun 13 12:11:57 2017 +0200 update email address --- debian/changelog | 1 + debian/control | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index 8568ee7..a67a2a6 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,6 +1,7 @@ snp-sites (2.3.3-1) unstable; urgency=medium * New upstream version. + * Update uploaders email address. -- Sascha Steinbiss <sa...@debian.org> Tue, 13 Jun 2017 12:10:53 +0200 diff --git a/debian/control b/debian/control index dfc8e64..31e1903 100644 --- a/debian/control +++ b/debian/control @@ -2,7 +2,7 @@ Source: snp-sites Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Uploaders: Jorge Soares <j.s.soa...@gmail.com>, Andreas Tille <ti...@debian.org>, - Sascha Steinbiss <sas...@steinbiss.name> + Sascha Steinbiss <sa...@debian.org> Section: science Priority: optional Build-Depends: debhelper (>= 9.0.0), -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snp-sites.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] [snp-sites] 03/04: new upstream version
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository snp-sites. commit 22fea134f978b5a9168187209a7152d763aca315 Author: Sascha Steinbiss <sa...@debian.org> Date: Tue Jun 13 12:11:14 2017 +0200 new upstream version --- debian/changelog | 6 ++ 1 file changed, 6 insertions(+) diff --git a/debian/changelog b/debian/changelog index b947868..8568ee7 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +snp-sites (2.3.3-1) unstable; urgency=medium + + * New upstream version. + + -- Sascha Steinbiss <sa...@debian.org> Tue, 13 Jun 2017 12:10:53 +0200 + snp-sites (2.3.2-1) unstable; urgency=medium * New upstream version. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snp-sites.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] [snp-sites] branch pristine-tar updated (44ac0f2 -> 47b6793)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch pristine-tar in repository snp-sites. from 44ac0f2 pristine-tar data for snp-sites_2.3.2.orig.tar.gz new 47b6793 pristine-tar data for snp-sites_2.3.3.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: snp-sites_2.3.3.orig.tar.gz.delta | Bin 0 -> 3414 bytes snp-sites_2.3.3.orig.tar.gz.id| 1 + 2 files changed, 1 insertion(+) create mode 100644 snp-sites_2.3.3.orig.tar.gz.delta create mode 100644 snp-sites_2.3.3.orig.tar.gz.id -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snp-sites.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] [snp-sites] 01/04: New upstream version 2.3.3
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch master
in repository snp-sites.
commit 298cfae1360903f9d56510eff595fb7a3b27ad4b
Author: Sascha Steinbiss <sa...@debian.org>
Date: Tue Jun 13 12:09:49 2017 +0200
New upstream version 2.3.3
---
AUTHORS | 2 +-
Dockerfile | 19 +++
LICENSE | 4
VERSION | 2 +-
src/alignment-file.c | 2 +-
src/snp-sites.c | 14 --
6 files changed, 34 insertions(+), 9 deletions(-)
diff --git a/AUTHORS b/AUTHORS
index 6d74363..bb6527c 100644
--- a/AUTHORS
+++ b/AUTHORS
@@ -1,3 +1,3 @@
Andrew J. Page <a...@sanger.ac.uk>
-Ben Taylor <b...@sanger.ac.uk>
+Ben Taylor <path-h...@sanger.ac.uk>
Jorge Soares <path-h...@sanger.ac.uk>
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 000..a1aeca3
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,19 @@
+#
+# From this base-image / starting-point
+#
+FROM debian:testing
+
+#
+# Authorship
+#
+MAINTAINER a...@sanger.ac.uk
+
+#
+# Pull in packages from testing
+#
+RUN apt-get update -qq
+
+#
+# Install Roary
+#
+RUN apt-get install snp-sites
diff --git a/LICENSE b/LICENSE
index c433dce..8050100 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,3 +1,7 @@
+Copyright (c) 2012 - 2016 by Genome Research Ltd.
+
+This is free software, licensed under:
+
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
diff --git a/VERSION b/VERSION
index f90b1af..0bee604 100644
--- a/VERSION
+++ b/VERSION
@@ -1 +1 @@
-2.3.2
+2.3.3
diff --git a/src/alignment-file.c b/src/alignment-file.c
index b1d83d7..01b73b6 100644
--- a/src/alignment-file.c
+++ b/src/alignment-file.c
@@ -184,7 +184,7 @@ void detect_snps(char filename[], int pure_mode, int
output_monomorphic)
}
int current_snp_index = 0;
- snp_locations = calloc(number_of_snps, sizeof(int));
+ snp_locations = calloc(number_of_snps +1, sizeof(int));
for(i = 0; i < length_of_genome; i++)
{
if(first_sequence[i] == '>' || (output_monomorphic && first_sequence[i]
!= '#'))
diff --git a/src/snp-sites.c b/src/snp-sites.c
index 8ce28aa..0f56224 100644
--- a/src/snp-sites.c
+++ b/src/snp-sites.c
@@ -27,6 +27,8 @@
#include "phylib-of-snp-sites.h"
#include "fasta-of-snp-sites.h"
+char ** bases_for_snps;
+
static int generate_snp_sites_generic(char filename[],
int output_multi_fasta_file,
int output_vcf_file,
@@ -37,20 +39,20 @@ static int generate_snp_sites_generic(char filename[],
int i;
detect_snps(filename, pure_mode, output_monomorphic);
- char* bases_for_snps[get_number_of_snps()];
-
+ bases_for_snps = calloc(get_number_of_snps()+1, sizeof(char*));
+
for(i = 0; i < get_number_of_snps(); i++)
{
- bases_for_snps[i] = calloc(get_number_of_samples()+1
,sizeof(char));
+ bases_for_snps[i] = calloc(get_number_of_samples()+1,
sizeof(char));
}
-
+
get_bases_for_each_snp(filename, bases_for_snps);
-
+
char output_filename_base[FILENAME_MAX];
char filename_without_directory[FILENAME_MAX];
strip_directory_from_filename(filename, filename_without_directory);
strncpy(output_filename_base, filename_without_directory, FILENAME_MAX);
-
+
if(output_filename != NULL && *output_filename != '\0')
{
strncpy(output_filename_base, output_filename, FILENAME_MAX);
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[med-svn] [rna-star] 02/02: new upstream release
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch experimental in repository rna-star. commit 947a0b42e9563ef8ae295c59d401f5fdd1e138dd Author: Sascha Steinbiss <sa...@debian.org> Date: Wed May 31 17:46:16 2017 +0200 new upstream release --- debian/changelog | 6 ++ 1 file changed, 6 insertions(+) diff --git a/debian/changelog b/debian/changelog index 3067b1f..438bd31 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +rna-star (2.5.3a+dfsg-1) experimental; urgency=medium + + * New upstream release. + + -- Sascha Steinbiss <sa...@debian.org> Wed, 31 May 2017 17:41:43 +0200 + rna-star (2.5.2b+dfsg-1) unstable; urgency=medium * New upstream release. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/rna-star.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] [rna-star] 01/01: pristine-tar data for rna-star_2.5.3a+dfsg.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 rna-star. commit a50d50cc6d5f0140e565cf8b58f1aa6ad03ff59c Author: Sascha Steinbiss <sa...@debian.org> Date: Wed May 31 17:41:15 2017 +0200 pristine-tar data for rna-star_2.5.3a+dfsg.orig.tar.xz --- rna-star_2.5.3a+dfsg.orig.tar.xz.delta | Bin 0 -> 5525 bytes rna-star_2.5.3a+dfsg.orig.tar.xz.id| 1 + 2 files changed, 1 insertion(+) diff --git a/rna-star_2.5.3a+dfsg.orig.tar.xz.delta b/rna-star_2.5.3a+dfsg.orig.tar.xz.delta new file mode 100644 index 000..cd74992 Binary files /dev/null and b/rna-star_2.5.3a+dfsg.orig.tar.xz.delta differ diff --git a/rna-star_2.5.3a+dfsg.orig.tar.xz.id b/rna-star_2.5.3a+dfsg.orig.tar.xz.id new file mode 100644 index 000..56deef8 --- /dev/null +++ b/rna-star_2.5.3a+dfsg.orig.tar.xz.id @@ -0,0 +1 @@ +44f84bc210019fdbcd282d7be353bcf35451e9d0 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/rna-star.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] [rna-star] branch pristine-tar updated (ee020bb -> a50d50c)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch pristine-tar in repository rna-star. from ee020bb pristine-tar data for rna-star_2.5.2b+dfsg.orig.tar.xz new a50d50c pristine-tar data for rna-star_2.5.3a+dfsg.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: rna-star_2.5.3a+dfsg.orig.tar.xz.delta | Bin 0 -> 5525 bytes rna-star_2.5.3a+dfsg.orig.tar.xz.id| 1 + 2 files changed, 1 insertion(+) create mode 100644 rna-star_2.5.3a+dfsg.orig.tar.xz.delta create mode 100644 rna-star_2.5.3a+dfsg.orig.tar.xz.id -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/rna-star.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] [rna-star] branch upstream updated (060cffa -> f253b49)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch upstream in repository rna-star. from 060cffa Imported Upstream version 2.5.2b+dfsg new f253b49 New upstream version 2.5.3a+dfsg 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: .travis.yml | 11 + CHANGES.md | 13 + README.md| 18 +- doc/STARmanual.pdf | Bin 251507 -> 264875 bytes extras/doc-latex/STARmanual.tex | 32 +- extras/doc-latex/parametersDefault.tex | 79 +- extras/scripts/tagXSstrandedData.awk | 35 + source/BAMbinSortByCoordinate.cpp|2 +- source/BAMbinSortUnmapped.cpp|2 +- source/Chain.cpp | 126 + source/Chain.h | 30 + source/Genome.cpp| 42 +- source/Genome.h |2 +- source/IncludeDefine.h |3 +- source/Makefile |2 +- source/Parameters.cpp| 134 +- source/Parameters.h | 34 +- source/ReadAlign_alignBAM.cpp| 14 +- source/ReadAlign_chimericDetection.cpp | 82 +- source/ReadAlign_multMapSelect.cpp |5 +- source/ReadAlign_outputAlignments.cpp|2 +- source/ReadAlign_outputTranscriptSAM.cpp |3 + source/STAR.cpp | 49 +- source/SharedMemory.cpp | 10 +- source/SharedMemory.h|2 +- source/VERSION |2 +- source/bamRemoveDuplicates.cpp | 37 +- source/genomeGenerate.cpp| 11 +- source/genomeParametersWrite.cpp |6 + source/parametersDefault | 27 +- source/parametersDefault.xxd | 4548 +++--- 31 files changed, 2979 insertions(+), 2384 deletions(-) create mode 100644 extras/scripts/tagXSstrandedData.awk create mode 100644 source/Chain.cpp create mode 100644 source/Chain.h -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/rna-star.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] [rna-star] annotated tag upstream/2.5.3a+dfsg created (now 8f9423a)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag upstream/2.5.3a+dfsg in repository rna-star. at 8f9423a (tag) tagging f253b4955401b0654476cbc4f7258a45dba74a6f (commit) replaces upstream/2.5.2b+dfsg tagged by Sascha Steinbiss on Wed May 31 17:41:15 2017 +0200 - Log - Upstream version 2.5.3a+dfsg Sascha Steinbiss (1): New upstream version 2.5.3a+dfsg --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/rna-star.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] [rna-star] 01/02: Merge tag 'upstream/2.5.3a+dfsg' into experimental
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch experimental in repository rna-star. commit 5bc6bcade343cc4f8ea77dc6a26cf55b1c81b2b7 Merge: b6ba5fd f253b49 Author: Sascha Steinbiss <sa...@debian.org> Date: Wed May 31 17:41:15 2017 +0200 Merge tag 'upstream/2.5.3a+dfsg' into experimental Upstream version 2.5.3a+dfsg .travis.yml | 11 + CHANGES.md | 13 + README.md| 18 +- doc/STARmanual.pdf | Bin 251507 -> 264875 bytes extras/doc-latex/STARmanual.tex | 32 +- extras/doc-latex/parametersDefault.tex | 79 +- extras/scripts/tagXSstrandedData.awk | 35 + source/BAMbinSortByCoordinate.cpp|2 +- source/BAMbinSortUnmapped.cpp|2 +- source/Chain.cpp | 126 + source/Chain.h | 30 + source/Genome.cpp| 42 +- source/Genome.h |2 +- source/IncludeDefine.h |3 +- source/Makefile |2 +- source/Parameters.cpp| 134 +- source/Parameters.h | 34 +- source/ReadAlign_alignBAM.cpp| 14 +- source/ReadAlign_chimericDetection.cpp | 82 +- source/ReadAlign_multMapSelect.cpp |5 +- source/ReadAlign_outputAlignments.cpp|2 +- source/ReadAlign_outputTranscriptSAM.cpp |3 + source/STAR.cpp | 49 +- source/SharedMemory.cpp | 10 +- source/SharedMemory.h|2 +- source/VERSION |2 +- source/bamRemoveDuplicates.cpp | 37 +- source/genomeGenerate.cpp| 11 +- source/genomeParametersWrite.cpp |6 + source/parametersDefault | 27 +- source/parametersDefault.xxd | 4548 +++--- 31 files changed, 2979 insertions(+), 2384 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/rna-star.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] [rna-star] branch experimental created (now 947a0b4)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch experimental in repository rna-star. at 947a0b4 new upstream release This branch includes the following new commits: new 5bc6bca Merge tag 'upstream/2.5.3a+dfsg' into experimental new 947a0b4 new upstream release The 2 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. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/rna-star.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] 10/10: new upstream release
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch experimental in repository ariba. commit 1f9b8f4e08e99dc569f44f9f1b95c42862ee25ef Author: Sascha Steinbiss <sa...@debian.org> Date: Mon May 29 17:03:22 2017 +0200 new upstream release --- debian/changelog | 6 ++ 1 file changed, 6 insertions(+) diff --git a/debian/changelog b/debian/changelog index 3f5999d..aad7043 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +ariba (2.9.4+ds-1) experimental; urgency=medium + + * New upstream version. + + -- Sascha Steinbiss <sa...@debian.org> Mon, 29 May 2017 16:58:51 +0200 + ariba (2.9.3+ds-1) experimental; urgency=medium * New upstream version. -- 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] 03/10: add dependencies
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch experimental
in repository ariba.
commit 9ae9d4719e6b3917e13c69a22a6d6ea94f013070
Author: Sascha Steinbiss <sascha.steinb...@dcso.de>
Date: Tue Apr 4 14:23:58 2017 +0200
add dependencies
---
debian/control | 4
1 file changed, 4 insertions(+)
diff --git a/debian/control b/debian/control
index 7d47e06..9261b9a 100644
--- a/debian/control
+++ b/debian/control
@@ -13,6 +13,8 @@ Build-Depends: debhelper (>= 9),
python3-pysam (>= 0.9.1),
python3-nose (>= 1.3),
python3-bs4 (>= 4.1.0),
+ python3-matplotlib,
+ python3-tk,
bowtie2 (>= 2.1.0),
cd-hit,
mash,
@@ -41,6 +43,8 @@ Depends: ${misc:Depends},
python3-dendropy (>= 4.2.0),
python3-pymummer (>= 0.10.2),
python3-pysam (>= 0.9.1),
+ python3-matplotlib,
+ python3-tk,
fastaq (>= 3.12.0),
Description: Antibiotic Resistance Identification By Assembly
ARIBA is a tool that identifies antibiotic resistance genes by running local
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[med-svn] [ariba] 08/10: new upstream version
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch experimental in repository ariba. commit 3817a8facf1d1f148298868ad417b0941bcfd100 Author: Sascha Steinbiss <sa...@debian.org> Date: Fri Apr 28 16:57:42 2017 +0200 new upstream version --- debian/changelog | 6 ++ 1 file changed, 6 insertions(+) diff --git a/debian/changelog b/debian/changelog index 3517ba3..3f5999d 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +ariba (2.9.3+ds-1) experimental; urgency=medium + + * New upstream version. + + -- Sascha Steinbiss <sa...@debian.org> Fri, 28 Apr 2017 16:54:06 +0200 + ariba (2.9.2+ds-1) experimental; urgency=medium * New upstream version. -- 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] 07/10: Merge tag 'upstream/2.9.3+ds' into experimental
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch experimental in repository ariba. commit 7364eeec3cab6affa6b55ce6428a79d156e0ed8e Merge: 1e966f2 6ca3cc2 Author: Sascha Steinbiss <sa...@debian.org> Date: Fri Apr 28 16:53:27 2017 +0200 Merge tag 'upstream/2.9.3+ds' into experimental Upstream version 2.9.3+ds ariba/pubmlst_getter.py | 10 +- ariba/tests/data/pubmlst_rename_seqs.expected.fa | 10 ++ ariba/tests/data/pubmlst_rename_seqs.in.fa | 10 ++ setup.py | 2 +- 4 files changed, 30 insertions(+), 2 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] 04/10: Merge tag 'upstream/2.9.2+ds' into experimental
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch experimental in repository ariba. commit 606d1e422e3bcd9ec4d092b606a5717daeb9c60f Merge: 9ae9d47 a3fddfd Author: Sascha Steinbiss <sa...@debian.org> Date: Thu Apr 27 10:00:55 2017 +0200 Merge tag 'upstream/2.9.2+ds' into experimental Upstream version 2.9.2+ds README.md | 22 +- ariba/assembly.py | 1 + ariba/cluster.py| 1 + ariba/clusters.py | 2 -- ariba/external_progs.py | 7 +++ ariba/mapping.py| 4 ariba/summary.py| 1 + ariba/tests/mapping_test.py | 3 +++ install_dependencies.sh | 10 +- setup.py| 2 +- 10 files changed, 36 insertions(+), 17 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] 01/10: new upstream release
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch experimental in repository ariba. commit 1aed5c73886bfa24f7f87298bfdd9e18f1f017fa Author: Sascha Steinbiss <sascha.steinb...@dcso.de> Date: Tue Apr 4 13:49:02 2017 +0200 new upstream release --- debian/changelog | 6 ++ 1 file changed, 6 insertions(+) diff --git a/debian/changelog b/debian/changelog index 03728a2..7102a5e 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +ariba (2.9.0+ds-1) UNRELEASED; urgency=medium + + * New upstream version. + + -- Sascha Steinbiss <sa...@debian.org> Tue, 04 Apr 2017 13:45:47 +0200 + ariba (2.7.2+ds-1) experimental; urgency=medium * Team upload. -- 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_2.9.4+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 ede05a91d7163eca6d7a5bd4111b323998854ffc Author: Sascha Steinbiss <sa...@debian.org> Date: Mon May 29 16:58:09 2017 +0200 pristine-tar data for ariba_2.9.4+ds.orig.tar.xz --- ariba_2.9.4+ds.orig.tar.xz.delta | Bin 0 -> 19202 bytes ariba_2.9.4+ds.orig.tar.xz.id| 1 + 2 files changed, 1 insertion(+) diff --git a/ariba_2.9.4+ds.orig.tar.xz.delta b/ariba_2.9.4+ds.orig.tar.xz.delta new file mode 100644 index 000..99f7d15 Binary files /dev/null and b/ariba_2.9.4+ds.orig.tar.xz.delta differ diff --git a/ariba_2.9.4+ds.orig.tar.xz.id b/ariba_2.9.4+ds.orig.tar.xz.id new file mode 100644 index 000..0c153fe --- /dev/null +++ b/ariba_2.9.4+ds.orig.tar.xz.id @@ -0,0 +1 @@ +e9656c4462fa4398c9026c815606bddd108a720e -- 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] [roary] 01/01: New upstream version 3.8.2+dfsg
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch upstream in repository roary. commit c94f09af9229b63920a1498583f191297614bd21 Author: Sascha Steinbiss <sa...@debian.org> Date: Mon May 29 16:38:33 2017 +0200 New upstream version 3.8.2+dfsg --- AUTHORS| 2 +- README.md | 26 +- dist.ini | 2 +- lib/Bio/Roary.pm | 2 ++ lib/Bio/Roary/CommandLine/Roary.pm | 8 +++- lib/Bio/Roary/External/Mcl.pm | 4 ++-- 6 files changed, 26 insertions(+), 18 deletions(-) diff --git a/AUTHORS b/AUTHORS index f9d4e15..021f90a 100644 --- a/AUTHORS +++ b/AUTHORS @@ -1,2 +1,2 @@ Andrew J. Page (a...@sanger.ac.uk) -Carla A. Cummins (c...@sanger.ac.uk) +Carla A. Cummins (path-h...@sanger.ac.uk) diff --git a/README.md b/README.md index 5a4f94f..a0758a8 100644 --- a/README.md +++ b/README.md @@ -1,11 +1,11 @@ -#Roary the pan genome pipeline +# Roary the pan genome pipeline For instructions on how to use the software, the input format and output formats, please see [the Roary website](http://sanger-pathogens.github.io/Roary). [](https://travis-ci.org/sanger-pathogens/Roary) Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods wou [...] -##Citation +## Citation "Roary: Rapid large-scale prokaryote pan genome analysis", Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill, Bioinformatics, (2015). doi: http://dx.doi.org/10.1093/bioinformatics/btv421 @@ -23,13 +23,13 @@ Theres are a number of dependancies required for Roary, with instructions specif If the installation fails please contact your system administrator. If you encounter a bug please let us know by emailing ro...@sanger.ac.uk . -##Ubuntu/Debian -###Debian Testing +## Ubuntu/Debian +### Debian Testing ``` sudo apt-get install roary ``` -###Ubuntu 14.04/16.04 +### Ubuntu 14.04/16.04 All the dependancies can be installed using apt and cpanm. Root permissions are required. Ubuntu 16.04 contains a package for Roary but it is frozen at v3.6.0. ``` @@ -37,13 +37,13 @@ sudo apt-get install bedtools cd-hit ncbi-blast+ mcl parallel cpanminus prank ma sudo cpanm -f Bio::Roary ``` -###Ubuntu 12.04 +### Ubuntu 12.04 Some of the software versions in apt are quite old so follow the instructions for [LinuxBrew](http://brew.sh/linuxbrew/) below. -##CentOS/RedHat +## CentOS/RedHat To install the dependancies, the easiest way is to install [LinuxBrew](http://brew.sh/linuxbrew/) using the steps for Fedora, then follow the steps below for installing Roary on LinuxBrew. -##Homebrew/Linuxbrew - OSX/Linux +## Homebrew/Linuxbrew - OSX/Linux Assuming you have [homebrew](http://brew.sh/) (OSX) or [linuxbrew](http://brew.sh/linuxbrew/) (Linux) setup and installed on your system: ``` @@ -52,21 +52,21 @@ brew install bedtools cd-hit blast mcl parallel prank mafft fasttree cpanm sudo cpanm -f Bio::Roary ``` -##GNU Guix +## GNU Guix Roary is not included in version in [Guix](https://www.gnu.org/software/guix) 0.11.0 so `guix pull` is currently required before installation. ``` guix pull guix package --install roary ``` -##Virtual Machine - OSX/Linux/Windows +## Virtual Machine - OSX/Linux/Windows Roary wont run natively on Windows but we have created virtual machine which has all of the software setup, including Prokka, along with the test datasets from the paper. It is based on [Bio-Linux 8](http://environmentalomics.org/bio-linux/). You need to first install [VirtualBox](https://www.virtualbox.org/), then load the virtual machine, using the 'File -> Import Appliance' menu option. The root password is 'manager'. ftp://ftp.sanger.ac.uk/pub/pathogens/pathogens-vm/pathogens-vm.latest.ova More importantly though, if your trying to do bioinformatics on Windows, your not going to get very far and you should seriously consider upgrading to Linux. -##Docker - OSX/Linux/Windows/Cloud +## Docker - OSX/Linux/Windows/Cloud We have a docker container which gets automatically built from the latest version of Roary in Debian Med. To install it: ``` @@ -78,7 +78,7 @@ To use it you would use a command such as this (substituting in your directories docker run --rm -it -v /hom
[med-svn] [roary] branch pristine-tar updated (675ee31 -> 6932111)
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[med-svn] [roary] 01/01: pristine-tar data for roary_3.8.2+dfsg.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 roary. commit 6932111f81343328f19dbe2f4cc35c7c376376e8 Author: Sascha Steinbiss <sa...@debian.org> Date: Mon May 29 16:38:39 2017 +0200 pristine-tar data for roary_3.8.2+dfsg.orig.tar.gz --- roary_3.8.2+dfsg.orig.tar.gz.delta | Bin 0 -> 379830 bytes roary_3.8.2+dfsg.orig.tar.gz.id| 1 + 2 files changed, 1 insertion(+) diff --git a/roary_3.8.2+dfsg.orig.tar.gz.delta b/roary_3.8.2+dfsg.orig.tar.gz.delta new file mode 100644 index 000..43af5d7 Binary files /dev/null and b/roary_3.8.2+dfsg.orig.tar.gz.delta differ diff --git a/roary_3.8.2+dfsg.orig.tar.gz.id b/roary_3.8.2+dfsg.orig.tar.gz.id new file mode 100644 index 000..921fb9c --- /dev/null +++ b/roary_3.8.2+dfsg.orig.tar.gz.id @@ -0,0 +1 @@ +56cb052c2cb336eb7b149607b413361ce674c7c5 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/roary.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] [roary] annotated tag upstream/3.8.2+dfsg created (now dcb771f)
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[med-svn] [roary] 01/02: Merge tag 'upstream/3.8.2+dfsg' into experimental
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch experimental in repository roary. commit 07e2034c457e0e22fea3c8428b33f0d4f3f73fa5 Merge: 08f9fa3 c94f09a Author: Sascha Steinbiss <sa...@debian.org> Date: Mon May 29 16:38:39 2017 +0200 Merge tag 'upstream/3.8.2+dfsg' into experimental Upstream version 3.8.2+dfsg AUTHORS| 2 +- README.md | 26 +- dist.ini | 2 +- lib/Bio/Roary.pm | 2 ++ lib/Bio/Roary/CommandLine/Roary.pm | 8 +++- lib/Bio/Roary/External/Mcl.pm | 4 ++-- 6 files changed, 26 insertions(+), 18 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/roary.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] [roary] branch upstream updated (1a1a97a -> c94f09a)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch upstream in repository roary. from 1a1a97a New upstream version 3.8.0+dfsg new c94f09a New upstream version 3.8.2+dfsg 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 +- README.md | 26 +- dist.ini | 2 +- lib/Bio/Roary.pm | 2 ++ lib/Bio/Roary/CommandLine/Roary.pm | 8 +++- lib/Bio/Roary/External/Mcl.pm | 4 ++-- 6 files changed, 26 insertions(+), 18 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/roary.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] [mash] annotated tag debian/1.1.1-2 created (now 982a602)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag debian/1.1.1-2 in repository mash. at 982a602 (tag) tagging dfd27c1ad001cd9fc7f64c9739df6fc1648da115 (commit) replaces debian/1.1.1-1 tagged by Sascha Steinbiss on Wed May 24 09:17:57 2017 + - Log - mash Debian release 1.1.1-2 -BEGIN PGP SIGNATURE- iQIzBAABCAAdFiEEWzS6WqtVB+kDQm6F6NN64vCfSHIFAlklT8UACgkQ6NN64vCf SHIwAA/+O6607zuW0u5E/9ZotD4q91aSjqmnQVvMaAGSOPiG7qc9/Qe8/T8ZSGPv CX8ZE4QLPWpkAp55qaybEV9hK79YFWYB1wSCB8K4FDJNnHQ7PAPtMgdbzvjsz0sB EqeGYT51omdre/IwXMCj3MS08tZZQ4cj+e++dD7UeWLseoTTAe2EqZ3u56qQuWga fDl4OnFfmWYMT/euKjfpMILX9O7m8MolVPXy20TOIvN3tHkhqq3eu+9nX5sFzO+Q 3FL62IRSkKSrx3AY7MIJLSyP2seDl2Tjo9ymsMyC+SOhV2pFxGmfPUJctPXyESmF zezJ/yXAT8TqNvPAbEPPBw62vfZl8snX587jUlrWs9h//Dktjw5kLc5JS4ZLequO ieKmp5gvsU4iFM24hdSHb6st6nOiquW9zWMHDbjjGgbndnvflE8M7G8k1L1ESZke z3SXBVNpxJnAI4pXhIvWyRprmAG1rJX5RbuA8GXsaqtZ9vz361dO9bIqc0iTahb5 161D8RFXhsfI/EnsJykXsPXvo3LZzsKWp50oeqCWHz8BwlZmjCu4oLcNgd4ydFRX 9Df2cQ69me9lSQtuO5SzAig5//zruUdSDKD8y14ORcIVhsy1OzMNjLSe/S8KNAg9 v7iyhH/zEByBbB5TNTIMC4tXTtJX2fXjNGQUUMCmS7pijmMZeys= =fixv -END PGP SIGNATURE- Sascha Steinbiss (1): fix parallel building FTBFS --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/mash.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] [mash] branch master updated (dc409d7 -> dfd27c1)
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[med-svn] [mash] 01/01: fix parallel building FTBFS
This is an automated email from the git hooks/post-receive script.
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commit dfd27c1ad001cd9fc7f64c9739df6fc1648da115
Author: Sascha Steinbiss <sa...@debian.org>
Date: Wed May 24 08:45:13 2017 +
fix parallel building FTBFS
---
debian/changelog | 7 +++
debian/patches/parallel.patch | 20
debian/patches/series | 1 +
3 files changed, 28 insertions(+)
diff --git a/debian/changelog b/debian/changelog
index 28c91f3..503439c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+mash (1.1.1-2) unstable; urgency=medium
+
+ * Fix parallel building FTBFS. Thanks to Adrian Bunk for the patch.
+Closes: #863208
+
+ -- Sascha Steinbiss <sa...@debian.org> Wed, 24 May 2017 08:43:17 +
+
mash (1.1.1-1) unstable; urgency=medium
* New upstream release.
diff --git a/debian/patches/parallel.patch b/debian/patches/parallel.patch
new file mode 100644
index 000..9cffb05
--- /dev/null
+++ b/debian/patches/parallel.patch
@@ -0,0 +1,20 @@
+Description: Fix parallel build failures
+ "capnp compile" ran twice, and in parallel builds twice in parallel.
+ This resulted in occasional build failures caused by corrupt output files.
+ .
+ Fix the Makefile to only run "capnp compile" once.
+Author: Adrian Bunk <b...@debian.org>
+
+--- mash-1.1.1.orig/Makefile.in
mash-1.1.1/Makefile.in
+@@ -46,7 +46,9 @@ libmash.a : $(OBJECTS)
+ %.o : %.c++
+ $(CXX) -c $(CXXFLAGS) $(CPPFLAGS) -o $@ $<
+
+-src/mash/capnp/MinHash.capnp.c++ src/mash/capnp/MinHash.capnp.h :
src/mash/capnp/MinHash.capnp
++src/mash/capnp/MinHash.capnp.c++ : src/mash/capnp/MinHash.capnp.h
++
++src/mash/capnp/MinHash.capnp.h : src/mash/capnp/MinHash.capnp
+ cd src/mash/capnp;export PATH=@capnp@/bin/:${PATH};capnp compile -I
@capnp@/include -oc++ MinHash.capnp
+
+ install : mash
diff --git a/debian/patches/series b/debian/patches/series
index 6776cfe..17700a6 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,3 +2,4 @@ hardening.patch
use_debian_mathjax.patch
drop_memcpy_wrapper.patch
link_dynamically_against_capnp.patch
+parallel.patch
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[med-svn] [ariba] annotated tag upstream/2.9.3+ds created (now d97584e)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag upstream/2.9.3+ds in repository ariba. at d97584e (tag) tagging 6ca3cc222a57d7c2ca74ca18c83f3f9cd4c686e3 (commit) replaces upstream/2.9.2+ds tagged by Sascha Steinbiss on Fri Apr 28 16:53:27 2017 +0200 - Log - Upstream version 2.9.3+ds Sascha Steinbiss (2): New upstream version 2.9.3+ds New upstream version 2.9.3+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] 01/02: pristine-tar data for ariba_2.9.3+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 4c179c6753286217074d25e07b9f3fefc068b663 Author: Sascha Steinbiss <sa...@debian.org> Date: Fri Apr 28 16:52:10 2017 +0200 pristine-tar data for ariba_2.9.3+ds.orig.tar.xz --- ariba_2.9.3+ds.orig.tar.xz.delta | Bin 0 -> 19180 bytes ariba_2.9.3+ds.orig.tar.xz.id| 1 + 2 files changed, 1 insertion(+) diff --git a/ariba_2.9.3+ds.orig.tar.xz.delta b/ariba_2.9.3+ds.orig.tar.xz.delta new file mode 100644 index 000..08f5718 Binary files /dev/null and b/ariba_2.9.3+ds.orig.tar.xz.delta differ diff --git a/ariba_2.9.3+ds.orig.tar.xz.id b/ariba_2.9.3+ds.orig.tar.xz.id new file mode 100644 index 000..259a02a --- /dev/null +++ b/ariba_2.9.3+ds.orig.tar.xz.id @@ -0,0 +1 @@ +4d30e31665432bf743e006aa0c4a0f1b57b7eeda -- 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] 02/02: pristine-tar data for ariba_2.9.3+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 6c02227b8d2c8d9b4d47e8504e84fe691c89fbd0 Author: Sascha Steinbiss <sa...@debian.org> Date: Fri Apr 28 16:53:27 2017 +0200 pristine-tar data for ariba_2.9.3+ds.orig.tar.xz --- ariba_2.9.3+ds.orig.tar.xz.delta | Bin 19180 -> 19186 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/ariba_2.9.3+ds.orig.tar.xz.delta b/ariba_2.9.3+ds.orig.tar.xz.delta index 08f5718..789cb44 100644 Binary files a/ariba_2.9.3+ds.orig.tar.xz.delta and b/ariba_2.9.3+ds.orig.tar.xz.delta differ -- 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] 01/02: New upstream version 2.9.3+ds
This is an automated email from the git hooks/post-receive script.
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commit db1f8f07c0943120e89024d8bd0c0117305c46bb
Author: Sascha Steinbiss <sa...@debian.org>
Date: Fri Apr 28 16:52:08 2017 +0200
New upstream version 2.9.3+ds
---
ariba/pubmlst_getter.py | 10 +-
ariba/tests/data/pubmlst_rename_seqs.expected.fa | 10 ++
ariba/tests/data/pubmlst_rename_seqs.in.fa | 10 ++
setup.py | 2 +-
4 files changed, 30 insertions(+), 2 deletions(-)
diff --git a/ariba/pubmlst_getter.py b/ariba/pubmlst_getter.py
index 0f794d1..6ac8bf5 100644
--- a/ariba/pubmlst_getter.py
+++ b/ariba/pubmlst_getter.py
@@ -1,4 +1,5 @@
import tempfile
+import re
import time
import os
import shutil
@@ -79,9 +80,16 @@ class PubmlstGetter:
def _rename_seqs_in_fasta(cls, infile, outfile):
f = pyfastaq.utils.open_file_write(outfile)
file_reader = pyfastaq.sequences.file_reader(infile)
+nodot_regex = re.compile(r'^.*(?P[^.0-9])[0-9]+$')
for seq in file_reader:
-seq.id = seq.id.replace('_', '.').replace('-', '.')
+if seq.id.startswith('Oxf.'):
+seq.id = 'Oxf_' + seq.id[4:]
+
+regex_match = nodot_regex.match(seq.id)
+if regex_match is not None:
+seq.id =
'.'.join(seq.id.rsplit(regex_match.groupdict()['separator'], maxsplit=1))
+
print(seq, file=f)
pyfastaq.utils.close(f)
diff --git a/ariba/tests/data/pubmlst_rename_seqs.expected.fa
b/ariba/tests/data/pubmlst_rename_seqs.expected.fa
index 7e7fa08..d6cb400 100644
--- a/ariba/tests/data/pubmlst_rename_seqs.expected.fa
+++ b/ariba/tests/data/pubmlst_rename_seqs.expected.fa
@@ -4,3 +4,13 @@ ACGT
>gene.3
+>foo_gene.4
+
+>Oxf_gltA.42
+A
+>Oxf_gltA.43
+C
+>Oxf_gltA.44
+G
+>Oxf_gltA.45
+T
diff --git a/ariba/tests/data/pubmlst_rename_seqs.in.fa
b/ariba/tests/data/pubmlst_rename_seqs.in.fa
index 8b1a4c7..16c443e 100644
--- a/ariba/tests/data/pubmlst_rename_seqs.in.fa
+++ b/ariba/tests/data/pubmlst_rename_seqs.in.fa
@@ -4,3 +4,13 @@ ACGT
>gene.3
+>foo_gene.4
+
+>Oxf.gltA.42
+A
+>Oxf.gltA-43
+C
+>Oxf.gltA_44
+G
+>Oxf.gltA?45
+T
diff --git a/setup.py b/setup.py
index 7c673d0..1f1d390 100644
--- a/setup.py
+++ b/setup.py
@@ -55,7 +55,7 @@ vcfcall_mod = Extension(
setup(
ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
name='ariba',
-version='2.9.2',
+version='2.9.3',
description='ARIBA: Antibiotic Resistance Identification By Assembly',
packages = find_packages(),
package_data={'ariba': ['test_run_data/*']},
--
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[med-svn] [ariba] 02/02: New upstream version 2.9.3+ds
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch upstream in repository ariba. commit 6ca3cc222a57d7c2ca74ca18c83f3f9cd4c686e3 Author: Sascha Steinbiss <sa...@debian.org> Date: Fri Apr 28 16:53:26 2017 +0200 New upstream version 2.9.3+ds -- 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 (a3fddfd -> 6ca3cc2)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch upstream in repository ariba. from a3fddfd New upstream version 2.9.2+ds new db1f8f0 New upstream version 2.9.3+ds new 6ca3cc2 New upstream version 2.9.3+ds The 2 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/pubmlst_getter.py | 10 +- ariba/tests/data/pubmlst_rename_seqs.expected.fa | 10 ++ ariba/tests/data/pubmlst_rename_seqs.in.fa | 10 ++ setup.py | 2 +- 4 files changed, 30 insertions(+), 2 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 pristine-tar updated (ffde06d -> 6c02227)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch pristine-tar in repository ariba. from ffde06d pristine-tar data for ariba_2.9.2+ds.orig.tar.xz new 4c179c6 pristine-tar data for ariba_2.9.3+ds.orig.tar.xz new 6c02227 pristine-tar data for ariba_2.9.3+ds.orig.tar.xz The 2 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_2.9.3+ds.orig.tar.xz.delta | Bin 0 -> 19186 bytes ariba_2.9.3+ds.orig.tar.xz.id| 1 + 2 files changed, 1 insertion(+) create mode 100644 ariba_2.9.3+ds.orig.tar.xz.delta create mode 100644 ariba_2.9.3+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] annotated tag upstream/2.9.0+ds created (now adcd7e6)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag upstream/2.9.0+ds in repository ariba. at adcd7e6 (tag) tagging b69312eb350eebfe9e444a0eae1a7dd959c1a1ef (commit) replaces upstream/2.7.2+ds tagged by Sascha Steinbiss on Tue Apr 4 14:09:02 2017 +0200 - Log - Upstream version 2.9.0+ds Sascha Steinbiss (2): New upstream version 2.9.0+ds New upstream version 2.9.0+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 upstream/2.9.2+ds created (now 6cb4d16)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag upstream/2.9.2+ds in repository ariba. at 6cb4d16 (tag) tagging a3fddfdbab4f6acdf9905d1bbeec7a677f9d9589 (commit) replaces upstream/2.9.0+ds tagged by Sascha Steinbiss on Thu Apr 27 10:00:55 2017 +0200 - Log - Upstream version 2.9.2+ds Sascha Steinbiss (1): New upstream version 2.9.2+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] 02/02: New upstream version 2.9.2+ds
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch upstream
in repository ariba.
commit a3fddfdbab4f6acdf9905d1bbeec7a677f9d9589
Author: Sascha Steinbiss <sa...@debian.org>
Date: Thu Apr 27 10:00:54 2017 +0200
New upstream version 2.9.2+ds
---
README.md | 22 +-
ariba/assembly.py | 1 +
ariba/cluster.py| 1 +
ariba/clusters.py | 2 --
ariba/external_progs.py | 7 +++
ariba/mapping.py| 4
ariba/summary.py| 1 +
ariba/tests/mapping_test.py | 3 +++
install_dependencies.sh | 10 +-
setup.py| 2 +-
10 files changed, 36 insertions(+), 17 deletions(-)
diff --git a/README.md b/README.md
index d67ab84..3b68744 100644
--- a/README.md
+++ b/README.md
@@ -1,16 +1,10 @@
-Disclaimer
-==
-
-This is pre-publication software that is currently under active development.
-Use it at your own risk. Bug reports are welcome, but
-user support is not provided at this time.
-
-
ARIBA
=
Antimicrobial Resistance Identification By Assembly
+For methods and benchmarking, please see the [preprint on biorxiv][ariba
biorxiv].
+
For how to use ARIBA, please see the [ARIBA wiki page][ARIBA wiki].
@@ -61,6 +55,16 @@ ARIBA is available in the latest version of Debian, and over
time will progressi
sudo apt-get install ariba
+### Ubuntu
+
+You can use `apt-get` (see above), or to ensure you get the latest version of
ARIBA, the following commands can be
+used to install ARIBA and its dependencies. This was tested on a new instance
of Ubuntu 16.04.
+
+sudo apt-get update
+sudo apt-get install -y python3-dev python3-pip python3-tk zlib1g-dev
bowtie2 mummer cd-hit
+export ARIBA_CDHIT=cdhit-est
+sudo pip3 install ariba
+
### Dependencies and environment variables
By default, ARIBA will look for the dependencies in your `$PATH`, using
@@ -135,7 +139,7 @@ Please read the [ARIBA wiki page][ARIBA wiki] for usage
instructions.
Build status: [](https://travis-ci.org/sanger-pathogens/ariba)
-
+ [ariba biorxiv]: http://biorxiv.org/content/early/2017/04/07/118000
[bowtie2]: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
[cdhit]: http://weizhongli-lab.org/cd-hit/
[ARIBA wiki]: https://github.com/sanger-pathogens/ariba/wiki
diff --git a/ariba/assembly.py b/ariba/assembly.py
index 721a932..f028a63 100644
--- a/ariba/assembly.py
+++ b/ariba/assembly.py
@@ -211,6 +211,7 @@ class Assembly:
threads=1,
sort=True,
bowtie2=self.extern_progs.exe('bowtie2'),
+bowtie2_version=self.extern_progs.version('bowtie2'),
verbose=True,
verbose_filehandle=self.log_fh
)
diff --git a/ariba/cluster.py b/ariba/cluster.py
index 6285513..75d244b 100644
--- a/ariba/cluster.py
+++ b/ariba/cluster.py
@@ -352,6 +352,7 @@ class Cluster:
sort=True,
bowtie2=self.extern_progs.exe('bowtie2'),
bowtie2_preset='very-sensitive-local',
+bowtie2_version=self.extern_progs.version('bowtie2'),
verbose=True,
verbose_filehandle=self.log_fh
)
diff --git a/ariba/clusters.py b/ariba/clusters.py
index b9c5756..ae50cd5 100644
--- a/ariba/clusters.py
+++ b/ariba/clusters.py
@@ -609,8 +609,6 @@ class Clusters:
print('{:_^79}'.format(' Cleaning files '), flush=True)
self._clean()
-print('self.mlst_profile_file', self.mlst_profile_file)
-print('self.report_file_filtered', self.report_file_filtered)
Clusters._write_mlst_reports(self.mlst_profile_file,
self.report_file_filtered, self.mlst_reports_prefix, verbose=self.verbose)
if self.clusters_all_ran_ok and self.verbose:
diff --git a/ariba/external_progs.py b/ariba/external_progs.py
index cb92393..dbbe077 100644
--- a/ariba/external_progs.py
+++ b/ariba/external_progs.py
@@ -38,6 +38,7 @@ class ExternalProgs:
self.progs = {}
self.version_report = []
self.all_deps_ok = True
+self.versions = {}
if verbose:
print('{:_^79}'.format(' Checking dependencies and their versions
'))
@@ -60,9 +61,11 @@ class ExternalProgs:
got_version, version = self._get_version(prog, self.progs[prog])
if got_version:
+self.versions[prog] = version
if prog in min_versions and LooseVersion(version) <
LooseVersion(min_versions[prog]):
errors.append(' '.join(['Found version', version, 'of',
prog, 'which is too low! Please update to at least', min_versions[prog] + '.
Found it here:', prog_exe]))
else:
+self.versions[prog] = None
errors.appen
[med-svn] [ariba] branch pristine-tar updated (43930dc -> ffde06d)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch pristine-tar in repository ariba. from 43930dc pristine-tar data for ariba_2.7.2+ds.orig.tar.xz new 587fdb8 pristine-tar data for ariba_2.9.0+ds.orig.tar.xz new 51f3765 pristine-tar data for ariba_2.9.0+ds.orig.tar.xz new ffde06d pristine-tar data for ariba_2.9.2+ds.orig.tar.xz 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_2.9.0+ds.orig.tar.xz.delta | Bin 0 -> 19153 bytes ariba_2.9.0+ds.orig.tar.xz.id| 1 + ariba_2.9.2+ds.orig.tar.xz.delta | Bin 0 -> 19108 bytes ariba_2.9.2+ds.orig.tar.xz.id| 1 + 4 files changed, 2 insertions(+) create mode 100644 ariba_2.9.0+ds.orig.tar.xz.delta create mode 100644 ariba_2.9.0+ds.orig.tar.xz.id create mode 100644 ariba_2.9.2+ds.orig.tar.xz.delta create mode 100644 ariba_2.9.2+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] branch upstream updated (eebec95 -> a3fddfd)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch upstream in repository ariba. from eebec95 New upstream version 2.7.2+ds new 83edd46 New upstream version 2.9.0+ds new b69312e New upstream version 2.9.0+ds new a3fddfd New upstream version 2.9.2+ds 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: README.md | 32 +- ariba/__init__.py | 1 + ariba/assembly.py | 1 + ariba/assembly_compare.py | 33 ++ ariba/assembly_variants.py | 23 +- ariba/cluster.py | 5 +- ariba/clusters.py | 2 - ariba/ext/vcfcall_ariba.cpp| 3 +- ariba/external_progs.py| 7 + ariba/mapping.py | 4 + ariba/mic_plotter.py | 651 + ariba/ref_genes_getter.py | 53 ++ ariba/summary.py | 38 +- ariba/summary_cluster.py | 23 +- ariba/summary_cluster_variant.py | 58 +- ariba/summary_sample.py| 2 +- ariba/tasks/__init__.py| 1 + ariba/tasks/micplot.py | 39 ++ ariba/tasks/summary.py | 10 +- ariba/tests/assembly_compare_test.py | 31 + ariba/tests/assembly_variants_test.py | 17 +- ariba/tests/data/mic_plotter_load_mic_file.tsv | 7 + ariba/tests/data/mic_plotter_load_summary_file.tsv | 3 + ...oxplot_tsv.antibio1.exclude.no_combinations.tsv | 3 + ...mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv | 2 + ..._to_boxplot_tsv.antibio1.no.no_combinations.tsv | 4 + .../mic_plotter_to_boxplot_tsv.antibio1.no.tsv | 3 + ...to_boxplot_tsv.antibio1.yes.no_combinations.tsv | 5 + .../mic_plotter_to_boxplot_tsv.antibio1.yes.tsv| 3 + ...oxplot_tsv.antibio2.exclude.no_combinations.tsv | 4 + ...mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv | 3 + ..._to_boxplot_tsv.antibio2.no.no_combinations.tsv | 4 + .../mic_plotter_to_boxplot_tsv.antibio2.no.tsv | 3 + ...to_boxplot_tsv.antibio2.yes.no_combinations.tsv | 4 + .../mic_plotter_to_boxplot_tsv.antibio2.yes.tsv| 3 + ariba/tests/data/summary_test_load_fofn| 4 + ariba/tests/data/summary_test_whole_run.out.csv| 6 +- ariba/tests/mapping_test.py| 3 + ariba/tests/mic_plotter_test.py| 283 + ariba/tests/summary_cluster_test.py| 16 +- ariba/tests/summary_cluster_variant_test.py| 104 ++-- ariba/tests/summary_sample_test.py | 9 +- ariba/tests/summary_test.py| 129 ++-- install_dependencies.sh| 10 +- scripts/ariba | 55 +- setup.py | 3 +- 46 files changed, 1529 insertions(+), 178 deletions(-) create mode 100644 ariba/mic_plotter.py create mode 100644 ariba/tasks/micplot.py create mode 100644 ariba/tests/data/mic_plotter_load_mic_file.tsv create mode 100644 ariba/tests/data/mic_plotter_load_summary_file.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv create mode 100644 ariba/tests/data/summary_test_load_fofn create mode 100644 ariba/tests/mic_plotter_test.py -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git
[med-svn] [ariba] 01/02: New upstream version 2.9.0+ds
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch upstream in repository ariba. commit b69312eb350eebfe9e444a0eae1a7dd959c1a1ef Author: Sascha Steinbiss <sascha.steinb...@dcso.de> Date: Tue Apr 4 14:09:01 2017 +0200 New upstream version 2.9.0+ds -- 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: pristine-tar data for ariba_2.9.2+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 ffde06d966b642913f2196e0945539cb9817f090 Author: Sascha Steinbiss <sa...@debian.org> Date: Thu Apr 27 10:00:55 2017 +0200 pristine-tar data for ariba_2.9.2+ds.orig.tar.xz --- ariba_2.9.2+ds.orig.tar.xz.delta | Bin 0 -> 19108 bytes ariba_2.9.2+ds.orig.tar.xz.id| 1 + 2 files changed, 1 insertion(+) diff --git a/ariba_2.9.2+ds.orig.tar.xz.delta b/ariba_2.9.2+ds.orig.tar.xz.delta new file mode 100644 index 000..c4393e0 Binary files /dev/null and b/ariba_2.9.2+ds.orig.tar.xz.delta differ diff --git a/ariba_2.9.2+ds.orig.tar.xz.id b/ariba_2.9.2+ds.orig.tar.xz.id new file mode 100644 index 000..1fd2280 --- /dev/null +++ b/ariba_2.9.2+ds.orig.tar.xz.id @@ -0,0 +1 @@ +708ee3f1a5457b955785bc19d0fcf9331002494c -- 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] 02/03: pristine-tar data for ariba_2.9.0+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 51f376570c7e19563298d6ab84f188fc9859099f Author: Sascha Steinbiss <sascha.steinb...@dcso.de> Date: Tue Apr 4 14:09:02 2017 +0200 pristine-tar data for ariba_2.9.0+ds.orig.tar.xz --- ariba_2.9.0+ds.orig.tar.xz.delta | Bin 19131 -> 19153 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/ariba_2.9.0+ds.orig.tar.xz.delta b/ariba_2.9.0+ds.orig.tar.xz.delta index e280c3d..421db09 100644 Binary files a/ariba_2.9.0+ds.orig.tar.xz.delta and b/ariba_2.9.0+ds.orig.tar.xz.delta differ -- 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] 02/02: Merge tag 'upstream/2.9.0+ds'
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch master in repository ariba. commit 8d2b3e7732a26894bcfef1ffa369b4feceb3d770 Merge: 285b94a 83edd46 Author: Sascha Steinbiss <sascha.steinb...@dcso.de> Date: Tue Apr 4 13:45:17 2017 +0200 Merge tag 'upstream/2.9.0+ds' Upstream version 2.9.0+ds README.md | 10 +- ariba/__init__.py | 1 + ariba/assembly_compare.py | 33 ++ ariba/assembly_variants.py | 23 +- ariba/cluster.py | 4 +- ariba/ext/vcfcall_ariba.cpp| 3 +- ariba/mic_plotter.py | 651 + ariba/ref_genes_getter.py | 53 ++ ariba/summary.py | 37 +- ariba/summary_cluster.py | 23 +- ariba/summary_cluster_variant.py | 58 +- ariba/summary_sample.py| 2 +- ariba/tasks/__init__.py| 1 + ariba/tasks/micplot.py | 39 ++ ariba/tasks/summary.py | 10 +- ariba/tests/assembly_compare_test.py | 31 + ariba/tests/assembly_variants_test.py | 17 +- ariba/tests/data/mic_plotter_load_mic_file.tsv | 7 + ariba/tests/data/mic_plotter_load_summary_file.tsv | 3 + ...oxplot_tsv.antibio1.exclude.no_combinations.tsv | 3 + ...mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv | 2 + ..._to_boxplot_tsv.antibio1.no.no_combinations.tsv | 4 + .../mic_plotter_to_boxplot_tsv.antibio1.no.tsv | 3 + ...to_boxplot_tsv.antibio1.yes.no_combinations.tsv | 5 + .../mic_plotter_to_boxplot_tsv.antibio1.yes.tsv| 3 + ...oxplot_tsv.antibio2.exclude.no_combinations.tsv | 4 + ...mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv | 3 + ..._to_boxplot_tsv.antibio2.no.no_combinations.tsv | 4 + .../mic_plotter_to_boxplot_tsv.antibio2.no.tsv | 3 + ...to_boxplot_tsv.antibio2.yes.no_combinations.tsv | 4 + .../mic_plotter_to_boxplot_tsv.antibio2.yes.tsv| 3 + ariba/tests/data/summary_test_load_fofn| 4 + ariba/tests/data/summary_test_whole_run.out.csv| 6 +- ariba/tests/mic_plotter_test.py| 283 + ariba/tests/summary_cluster_test.py| 16 +- ariba/tests/summary_cluster_variant_test.py| 104 ++-- ariba/tests/summary_sample_test.py | 9 +- ariba/tests/summary_test.py| 129 ++-- scripts/ariba | 55 +- setup.py | 3 +- 40 files changed, 1494 insertions(+), 162 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] 01/03: pristine-tar data for ariba_2.9.0+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 587fdb8c2228409f722f5ccb6fc5350b02dc603e Author: Sascha Steinbiss <sascha.steinb...@dcso.de> Date: Tue Apr 4 13:45:16 2017 +0200 pristine-tar data for ariba_2.9.0+ds.orig.tar.xz --- ariba_2.9.0+ds.orig.tar.xz.delta | Bin 0 -> 19131 bytes ariba_2.9.0+ds.orig.tar.xz.id| 1 + 2 files changed, 1 insertion(+) diff --git a/ariba_2.9.0+ds.orig.tar.xz.delta b/ariba_2.9.0+ds.orig.tar.xz.delta new file mode 100644 index 000..e280c3d Binary files /dev/null and b/ariba_2.9.0+ds.orig.tar.xz.delta differ diff --git a/ariba_2.9.0+ds.orig.tar.xz.id b/ariba_2.9.0+ds.orig.tar.xz.id new file mode 100644 index 000..be09ef9 --- /dev/null +++ b/ariba_2.9.0+ds.orig.tar.xz.id @@ -0,0 +1 @@ +30347078038509bcf76ddb3a66dfdd077f124d0c -- 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 (285b94a -> 8d2b3e7)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch master in repository ariba. from 285b94a Realise that 2.7.2+ds-1 was not yet uploaded - fix changelog and re-upload to experimental new 83edd46 New upstream version 2.9.0+ds new 8d2b3e7 Merge tag 'upstream/2.9.0+ds' The 2 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: README.md | 10 +- ariba/__init__.py | 1 + ariba/assembly_compare.py | 33 ++ ariba/assembly_variants.py | 23 +- ariba/cluster.py | 4 +- ariba/ext/vcfcall_ariba.cpp| 3 +- ariba/mic_plotter.py | 651 + ariba/ref_genes_getter.py | 53 ++ ariba/summary.py | 37 +- ariba/summary_cluster.py | 23 +- ariba/summary_cluster_variant.py | 58 +- ariba/summary_sample.py| 2 +- ariba/tasks/__init__.py| 1 + ariba/tasks/micplot.py | 39 ++ ariba/tasks/summary.py | 10 +- ariba/tests/assembly_compare_test.py | 31 + ariba/tests/assembly_variants_test.py | 17 +- ariba/tests/data/mic_plotter_load_mic_file.tsv | 7 + ariba/tests/data/mic_plotter_load_summary_file.tsv | 3 + ...oxplot_tsv.antibio1.exclude.no_combinations.tsv | 3 + ...mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv | 2 + ..._to_boxplot_tsv.antibio1.no.no_combinations.tsv | 4 + .../mic_plotter_to_boxplot_tsv.antibio1.no.tsv | 3 + ...to_boxplot_tsv.antibio1.yes.no_combinations.tsv | 5 + .../mic_plotter_to_boxplot_tsv.antibio1.yes.tsv| 3 + ...oxplot_tsv.antibio2.exclude.no_combinations.tsv | 4 + ...mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv | 3 + ..._to_boxplot_tsv.antibio2.no.no_combinations.tsv | 4 + .../mic_plotter_to_boxplot_tsv.antibio2.no.tsv | 3 + ...to_boxplot_tsv.antibio2.yes.no_combinations.tsv | 4 + .../mic_plotter_to_boxplot_tsv.antibio2.yes.tsv| 3 + ariba/tests/data/summary_test_load_fofn| 4 + ariba/tests/data/summary_test_whole_run.out.csv| 6 +- ariba/tests/mic_plotter_test.py| 283 + ariba/tests/summary_cluster_test.py| 16 +- ariba/tests/summary_cluster_variant_test.py| 104 ++-- ariba/tests/summary_sample_test.py | 9 +- ariba/tests/summary_test.py| 129 ++-- scripts/ariba | 55 +- setup.py | 3 +- 40 files changed, 1494 insertions(+), 162 deletions(-) create mode 100644 ariba/mic_plotter.py create mode 100644 ariba/tasks/micplot.py create mode 100644 ariba/tests/data/mic_plotter_load_mic_file.tsv create mode 100644 ariba/tests/data/mic_plotter_load_summary_file.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.no_combinations.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.exclude.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.no_combinations.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.no.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.no_combinations.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio1.yes.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.no_combinations.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.exclude.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.no_combinations.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.no.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.no_combinations.tsv create mode 100644 ariba/tests/data/mic_plotter_to_boxplot_tsv.antibio2.yes.tsv create mode 100644 ariba/tests/data/summary_test_load_fofn create mode 100644 ariba/tests/mic_plotter_test.py -- 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] [libhat-trie] branch pristine-tar updated (cc26bae -> c764154)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch pristine-tar in repository libhat-trie. from cc26bae pristine-tar data for libhat-trie_0.0~git25f9e946.orig.tar.bz2 new c764154 pristine-tar data for libhat-trie_0.1.1.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: libhat-trie_0.1.1.orig.tar.gz.delta | Bin 0 -> 1653 bytes libhat-trie_0.1.1.orig.tar.gz.id| 1 + 2 files changed, 1 insertion(+) create mode 100644 libhat-trie_0.1.1.orig.tar.gz.delta create mode 100644 libhat-trie_0.1.1.orig.tar.gz.id -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libhat-trie.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] [libhat-trie] branch experimental created (now f76bda5)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch experimental in repository libhat-trie. at f76bda5 refresh patches This branch includes the following new commits: new 455bff8 Merge tag 'upstream/0.1.1' into experimental new 08efea9 new upstream release new f76bda5 refresh patches 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. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libhat-trie.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] [libhat-trie] 01/03: Merge tag 'upstream/0.1.1' into experimental
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch experimental in repository libhat-trie. commit 455bff888ca779c3d77649457f891ef85e6b50e3 Merge: 6dfa78e 3c6fb6e Author: Sascha Steinbiss <sascha.steinb...@dcso.de> Date: Tue Apr 25 10:27:10 2017 +0200 Merge tag 'upstream/0.1.1' into experimental Upstream version 0.1.1 configure.ac | 4 +- src/ahtable.c | 83 src/ahtable.h | 4 ++ src/hat-trie.h| 1 - src/portable_endian.h | 116 ++ test/check_ahtable.c | 51 ++ 6 files changed, 256 insertions(+), 3 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libhat-trie.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] [libhat-trie] 02/03: new upstream release
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch experimental in repository libhat-trie. commit 08efea9c5cc1a2855ec97e0b962dee102f184560 Author: Sascha Steinbiss <sascha.steinb...@dcso.de> Date: Tue Apr 25 10:33:44 2017 +0200 new upstream release --- debian/changelog | 7 +++ debian/copyright | 7 +++ 2 files changed, 14 insertions(+) diff --git a/debian/changelog b/debian/changelog index 00b6f9f..f3e3fd8 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +libhat-trie (0.1.1-1) experimental; urgency=medium + + * New versioned upstream release. + * Add new public domain file to d/copyright. + + -- Sascha Steinbiss <sa...@debian.org> Tue, 25 Apr 2017 10:33:07 +0200 + libhat-trie (0.0~git25f9e946-2) unstable; urgency=medium * Make build reproducible. diff --git a/debian/copyright b/debian/copyright index 7047dbb..8399042 100644 --- a/debian/copyright +++ b/debian/copyright @@ -17,6 +17,13 @@ License: public-domain The original C++ code was placed in the public domain by its author, Austin Appleby. +Files: src/portable_endian.h +Copyright: Mathias Panzenböck +License: public-domain + Author statement is "I, Mathias Panzenböck, place this file + hereby into the public domain. Use it at your own risk for whatever + you like." + Files: src/pstdint.h Copyright: (c) 2005-2014 Paul Hsieh License: BSD-3-clause -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libhat-trie.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] [libhat-trie] 01/01: New upstream version 0.1.1
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch upstream
in repository libhat-trie.
commit 3c6fb6e692924f64bafa359f857fb54a307bb8c9
Author: Sascha Steinbiss <sascha.steinb...@dcso.de>
Date: Tue Apr 25 10:27:10 2017 +0200
New upstream version 0.1.1
---
configure.ac | 4 +-
src/ahtable.c | 83
src/ahtable.h | 4 ++
src/hat-trie.h| 1 -
src/portable_endian.h | 116 ++
test/check_ahtable.c | 51 ++
6 files changed, 256 insertions(+), 3 deletions(-)
diff --git a/configure.ac b/configure.ac
index 870b786..8acc767 100644
--- a/configure.ac
+++ b/configure.ac
@@ -1,10 +1,10 @@
-AC_INIT([hat-trie], [0.1.0], [dcjo...@cs.washington.edu])
+AC_INIT([hat-trie], [0.1.1], [dcjo...@cs.washington.edu])
AM_INIT_AUTOMAKE([foreign])
m4_ifdef([AM_SILENT_RULES],[AM_SILENT_RULES([yes])])
AC_CONFIG_MACRO_DIR([m4])
-base_CFLAGS="-std=c99 -Wall -Wextra -pedantic"
+base_CFLAGS="-std=gnu99 -Wall -Wextra -pedantic"
opt_CFLAGS="${base_CFLAGS} -O3"
dbg_CFLAGS="${base_CFLAGS} -g -O0"
diff --git a/src/ahtable.c b/src/ahtable.c
index c0f6fb3..8f9c23d 100644
--- a/src/ahtable.c
+++ b/src/ahtable.c
@@ -10,6 +10,7 @@
#include "ahtable.h"
#include "misc.h"
#include "murmurhash3.h"
+#include "portable_endian.h"
#include
#include
@@ -50,6 +51,83 @@ ahtable_t* ahtable_create_n(size_t n)
return table;
}
+void ahtable_save(const ahtable_t* table, FILE* fd)
+{
+if (table == NULL) return;
+
+/* Store table metadata as 64-bit network-ordered (big-endian) values so
+ * that architectures with larger capacity can take advantage of size.
+ */
+uint64_t n = htobe64(table->n);
+fwrite(, sizeof(uint64_t), 1, fd);
+
+uint64_t m = htobe64(table->m);
+fwrite(, sizeof(uint64_t), 1, fd);
+
+uint64_t max_m = htobe64(table->max_m);
+fwrite(_m, sizeof(uint64_t), 1, fd);
+
+fwrite(>flag, sizeof(uint8_t), 1, fd);
+
+fwrite(>c0, sizeof(unsigned char), 1, fd);
+fwrite(>c1, sizeof(unsigned char), 1, fd);
+
+size_t i;
+uint32_t slot_size;
+for (i = 0; i < table->n; ++i) {
+slot_size = htobe32(table->slot_sizes[i]);
+fwrite(_size, sizeof(uint32_t), 1, fd);
+if(table->slot_sizes[i] > 0) {
+fwrite(table->slots[i], sizeof(unsigned char),
table->slot_sizes[i], fd);
+}
+}
+}
+
+/* Loads a 64-bit value from disk and casts it into a size_t, which may or may
+ * not be 64-bit. As long as the loaded value fits inside size_t, we're good.
+ * Returns 0 if the value didn't fit, 1 otherwise.
+ */
+static uint8_t read_u64bit_to_size_t(size_t* dest, FILE* fd)
+{
+uint64_t value;
+fread(, sizeof(uint64_t), 1, fd);
+if (value > (size_t)-1) {
+printf("Unable to load 64-bit data from file\n");
+return 0;
+} else {
+*dest = (size_t)be64toh(value);
+return 1;
+}
+}
+
+ahtable_t* ahtable_load(FILE* fd)
+{
+size_t n;
+if (!read_u64bit_to_size_t(, fd)) return NULL;
+ahtable_t* table = ahtable_create_n(n);
+
+if (!read_u64bit_to_size_t(>m, fd)) return NULL;
+
+if (!read_u64bit_to_size_t(>max_m, fd)) return NULL;
+
+fread(>flag, sizeof(uint8_t), 1, fd);
+
+fread(>c0, sizeof(unsigned char), 1, fd);
+fread(>c1, sizeof(unsigned char), 1, fd);
+
+size_t i;
+uint32_t slot_size;
+for (i = 0; i < table->n; ++i) {
+fread(_size, sizeof(uint32_t), 1, fd);
+table->slot_sizes[i] = be32toh(slot_size);
+if(table->slot_sizes[i] > 0) {
+table->slots[i] = malloc_or_die(table->slot_sizes[i]);
+fread(table->slots[i], sizeof(unsigned char),
table->slot_sizes[i], fd);
+}
+}
+
+return table;
+}
void ahtable_free(ahtable_t* table)
{
@@ -259,6 +337,11 @@ static value_t* get_key(ahtable_t* table, const char* key,
size_t len, bool inse
value_t* ahtable_get(ahtable_t* table, const char* key, size_t len)
{
+if (len > 32767) {
+fprintf(stderr, "HAT-trie/AH-table cannot store keys longer than
32768\n");
+exit(EXIT_FAILURE);
+}
+
return get_key(table, key, len, true);
}
diff --git a/src/ahtable.h b/src/ahtable.h
index 15e8e21..c267d6c 100644
--- a/src/ahtable.h
+++ b/src/ahtable.h
@@ -47,6 +47,7 @@ extern "C" {
#include
#include
+#include
#include "pstdint.h"
#include "common.h"
@@ -74,6 +75,9 @@ ahtable_t* ahtable_create (void); // Create an
empty hash table.
ahtable_t* ahtable_create_n (size_t n); // Create an empty hash table, with
// n slots reserved.
+ahtable_t* ahtable_load (FILE*
[med-svn] [libhat-trie] annotated tag upstream/0.1.1 created (now f403742)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag upstream/0.1.1 in repository libhat-trie. at f403742 (tag) tagging 3c6fb6e692924f64bafa359f857fb54a307bb8c9 (commit) replaces upstream/0.0_git25f9e946 tagged by Sascha Steinbiss on Tue Apr 25 10:27:10 2017 +0200 - Log - Upstream version 0.1.1 Sascha Steinbiss (1): New upstream version 0.1.1 --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libhat-trie.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] [libhat-trie] 01/01: pristine-tar data for libhat-trie_0.1.1.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 libhat-trie. commit c764154defbc5d42bdd00f44c197d02cc207af83 Author: Sascha Steinbiss <sascha.steinb...@dcso.de> Date: Tue Apr 25 10:27:10 2017 +0200 pristine-tar data for libhat-trie_0.1.1.orig.tar.gz --- libhat-trie_0.1.1.orig.tar.gz.delta | Bin 0 -> 1653 bytes libhat-trie_0.1.1.orig.tar.gz.id| 1 + 2 files changed, 1 insertion(+) diff --git a/libhat-trie_0.1.1.orig.tar.gz.delta b/libhat-trie_0.1.1.orig.tar.gz.delta new file mode 100644 index 000..cc115c0 Binary files /dev/null and b/libhat-trie_0.1.1.orig.tar.gz.delta differ diff --git a/libhat-trie_0.1.1.orig.tar.gz.id b/libhat-trie_0.1.1.orig.tar.gz.id new file mode 100644 index 000..2bb3435 --- /dev/null +++ b/libhat-trie_0.1.1.orig.tar.gz.id @@ -0,0 +1 @@ +4bf60f9baf4b169f8340b3d64cba8f282d55 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libhat-trie.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] [libhat-trie] 03/03: refresh patches
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch experimental
in repository libhat-trie.
commit f76bda59c3a32699fbc654b5e9921a3c46abf9e9
Author: Sascha Steinbiss <sascha.steinb...@dcso.de>
Date: Tue Apr 25 10:45:45 2017 +0200
refresh patches
---
debian/patches/reproducible.patch | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/debian/patches/reproducible.patch
b/debian/patches/reproducible.patch
index 19e099e..7ea9f65 100644
--- a/debian/patches/reproducible.patch
+++ b/debian/patches/reproducible.patch
@@ -6,8 +6,8 @@ Author: Sascha Steinbiss <sas...@steinbiss.name>
m4_ifdef([AM_SILENT_RULES],[AM_SILENT_RULES([yes])])
AC_CONFIG_MACRO_DIR([m4])
--base_CFLAGS="-std=c99 -Wall -Wextra -pedantic"
-+base_CFLAGS="${CFLAGS} -std=c99 -Wall -Wextra -pedantic"
+-base_CFLAGS="-std=gnu99 -Wall -Wextra -pedantic"
++base_CFLAGS="${CFLAGS} ${CPPFLAGS} -std=gnu99 -Wall -Wextra -pedantic"
opt_CFLAGS="${base_CFLAGS} -O3"
dbg_CFLAGS="${base_CFLAGS} -g -O0"
--
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[med-svn] [libhat-trie] branch upstream updated (3a65669 -> 3c6fb6e)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch upstream in repository libhat-trie. from 3a65669 Imported Upstream version 0.0~git25f9e946 new 3c6fb6e New upstream version 0.1.1 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: configure.ac | 4 +- src/ahtable.c | 83 src/ahtable.h | 4 ++ src/hat-trie.h| 1 - src/portable_endian.h | 116 ++ test/check_ahtable.c | 51 ++ 6 files changed, 256 insertions(+), 3 deletions(-) create mode 100644 src/portable_endian.h -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libhat-trie.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] [spades] branch experimental created (now 556fb32)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch experimental in repository spades. at 556fb32 build for experimental This branch includes the following new commits: new 556fb32 build for experimental 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. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.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] [spades] 01/01: build for experimental
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch experimental in repository spades. commit 556fb32cfe799c88f08d5501acbcf69de86cce06 Author: Sascha Steinbiss <sa...@debian.org> Date: Fri Apr 21 17:54:48 2017 + build for experimental --- debian/changelog | 8 ++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/debian/changelog b/debian/changelog index 940d3ea..f04ddad 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,8 +1,12 @@ -spades (3.10.1+dfsg-1) UNRELEASED; urgency=medium +spades (3.10.1+dfsg-1) experimental; urgency=medium + [ Michael R. Crusoe ] * New upstream version 3.10.1+dfsg - -- Michael R. Crusoe <michael.cru...@gmail.com> Tue, 18 Apr 2017 03:37:47 -0700 + [ Sascha Steinbiss ] + * Build for experimental. + + -- Sascha Steinbiss <sa...@debian.org> Fri, 21 Apr 2017 17:54:15 + spades (3.9.1+dfsg-1) unstable; urgency=medium -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.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] [barrnap] annotated tag upstream/0.8 created (now a5bf674)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag upstream/0.8 in repository barrnap. at a5bf674 (tag) tagging cb478cc26ce031325a5406d10702426e8ba272ef (commit) replaces upstream/0.7+dfsg tagged by Sascha Steinbiss on Sun Apr 9 08:11:41 2017 + - Log - Upstream version 0.8 Sascha Steinbiss (1): New upstream version 0.8 --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/barrnap.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] [barrnap] 05/06: Merge branch 'master' of ssh://git.debian.org/git/debian-med/barrnap
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch experimental in repository barrnap. commit b05a5fe37f46fc8fe93e79730a2d9f9ae5188186 Merge: a4b6f54 67cd052 Author: Sascha Steinbiss <sa...@debian.org> Date: Sun Apr 9 08:47:51 2017 + Merge branch 'master' of ssh://git.debian.org/git/debian-med/barrnap debian/upstream/edam | 11 ++- 1 file changed, 6 insertions(+), 5 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/barrnap.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] [barrnap] annotated tag upstream/0.8+dfsg created (now df2fc9e)
This is an automated email from the git hooks/post-receive script. satta pushed a change to annotated tag upstream/0.8+dfsg in repository barrnap. at df2fc9e (tag) tagging f1e4e6f13e12ddd6cc15259e89e56ca2b8b37c4b (commit) replaces upstream/0.8 tagged by Sascha Steinbiss on Sun Apr 9 08:38:11 2017 + - Log - Upstream version 0.8+dfsg Sascha Steinbiss (1): New upstream version 0.8+dfsg --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/barrnap.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] [barrnap] 04/06: refresh patch
This is an automated email from the git hooks/post-receive script.
satta pushed a commit to branch experimental
in repository barrnap.
commit a4b6f54f9af6aa45b433f7b5ef9415528c3500cf
Author: Sascha Steinbiss <sa...@debian.org>
Date: Sun Apr 9 08:47:19 2017 +
refresh patch
---
debian/patches/use_debian_dirs | 14 --
1 file changed, 4 insertions(+), 10 deletions(-)
diff --git a/debian/patches/use_debian_dirs b/debian/patches/use_debian_dirs
index 1e31962..914f98e 100644
--- a/debian/patches/use_debian_dirs
+++ b/debian/patches/use_debian_dirs
@@ -1,19 +1,13 @@
Description: Do not rely on path location relative to barrnap executable
--- a/bin/barrnap
+++ b/bin/barrnap
-@@ -14,9 +14,14 @@
+@@ -14,6 +14,9 @@
my $AUTHOR = 'Torsten Seemann <torsten.seem...@gmail.com>';
- my $URL = 'https://github.com/Victorian-Bioinformatics-Consortium/barrnap';
+ my $URL = 'https://github.com/tseemann/barrnap';
my $DBDIR = "$FindBin::RealBin/../db";
+if ( ! -e $DBDIR) {
+ $DBDIR = "/usr/share/barrnap/db";
+}
my $OPSYS = $^O;
- my $NHMMER = "$FindBin::RealBin/../binaries/$OPSYS/nhmmer";
--
-+if ( ! -e $NHMMER ) {
-+ $NHMMER = "/usr/bin/nhmmer";
-+}
- my %KINGDOM = (map { substr($_,0,1) => $_ } qw(bac arc euk mito));
- my %LENG = (
- "5S_rRNA" =>119, "16S_rRNA"=>1585, "23S_rRNA"=>3232,
+ my $BINDIR = "$FindBin::RealBin/../binaries/$OPSYS";
+
--
Alioth's /usr/local/bin/git-commit-notice on
/srv/git.debian.org/git/debian-med/barrnap.git
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[med-svn] [barrnap] 06/06: bump Standards-Version
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch experimental in repository barrnap. commit d453a3ae2fa538f4aadca3db87188b16a80ccbc3 Author: Sascha Steinbiss <sa...@debian.org> Date: Sun Apr 9 08:52:18 2017 + bump Standards-Version --- debian/changelog | 3 ++- debian/control | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/debian/changelog b/debian/changelog index 48b23b7..0bd81b4 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,7 +1,8 @@ -barrnap (0.8+dfsg-1) UNRELEASED; urgency=medium +barrnap (0.8+dfsg-1) experimental; urgency=medium * New upstream release. * Adjust maintainer email address. + * Bump Standards-Version. -- Sascha Steinbiss <sa...@debian.org> Sun, 09 Apr 2017 08:34:19 + diff --git a/debian/control b/debian/control index 465b969..fcf69d6 100644 --- a/debian/control +++ b/debian/control @@ -4,7 +4,7 @@ Section: science Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Uploaders: Sascha Steinbiss <sa...@debian.org> Build-Depends: debhelper (>= 9.0.0), hmmer (>= 3.1), lua5.1 -Standards-Version: 3.9.7 +Standards-Version: 3.9.8 Homepage: http://www.vicbioinformatics.com/software.barrnap.shtml Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/barrnap.git Vcs-Git: https://anonscm.debian.org/git/debian-med/barrnap.git -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/barrnap.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] [barrnap] 03/06: Merge tag 'upstream/0.8+dfsg'
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch experimental in repository barrnap. commit 9572f353a595b4883f74b29f29a5e540ac40daf5 Merge: 1d17ab1 f1e4e6f Author: Sascha Steinbiss <sa...@debian.org> Date: Sun Apr 9 08:38:11 2017 + Merge tag 'upstream/0.8+dfsg' Upstream version 0.8+dfsg db/arc.hmm | 8957 --- db/bac.hmm | 8741 -- db/euk.hmm | 11210 --- 3 files changed, 28908 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/barrnap.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] [barrnap] 01/06: Merge tag 'upstream/0.8'
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch experimental in repository barrnap. commit 5ed942dd8826fdec0bd0e0439d507e65f2a7e748 Merge: 5923275 cb478cc Author: Sascha Steinbiss <sa...@debian.org> Date: Sun Apr 9 08:11:41 2017 + Merge tag 'upstream/0.8' Upstream version 0.8 bin/barrnap |14 +- db/arc.hmm | 15959 ++ db/bac.hmm | 15729 + db/euk.hmm | 16952 ++ db/mito.hmm | 14278 ++--- 5 files changed, 42462 insertions(+), 20470 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/barrnap.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] [barrnap] 02/06: new upstream version
This is an automated email from the git hooks/post-receive script. satta pushed a commit to branch experimental in repository barrnap. commit 1d17ab1d19ba7ca1c685e215d7877b9817a12ffa Author: Sascha Steinbiss <sa...@debian.org> Date: Sun Apr 9 08:37:23 2017 + new upstream version --- debian/changelog | 7 +++ debian/control | 2 +- 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index 95c2b77..48b23b7 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +barrnap (0.8+dfsg-1) UNRELEASED; urgency=medium + + * New upstream release. + * Adjust maintainer email address. + + -- Sascha Steinbiss <sa...@debian.org> Sun, 09 Apr 2017 08:34:19 + + barrnap (0.7+dfsg-2) unstable; urgency=medium [Afif Elghraoui] diff --git a/debian/control b/debian/control index 369627e..465b969 100644 --- a/debian/control +++ b/debian/control @@ -2,7 +2,7 @@ Source: barrnap Priority: optional Section: science Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> -Uploaders: Sascha Steinbiss <sas...@steinbiss.name> +Uploaders: Sascha Steinbiss <sa...@debian.org> Build-Depends: debhelper (>= 9.0.0), hmmer (>= 3.1), lua5.1 Standards-Version: 3.9.7 Homepage: http://www.vicbioinformatics.com/software.barrnap.shtml -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/barrnap.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] [barrnap] branch experimental created (now d453a3a)
This is an automated email from the git hooks/post-receive script. satta pushed a change to branch experimental in repository barrnap. at d453a3a bump Standards-Version This branch includes the following new commits: new 5ed942d Merge tag 'upstream/0.8' new 1d17ab1 new upstream version new 9572f35 Merge tag 'upstream/0.8+dfsg' new a4b6f54 refresh patch new b05a5fe Merge branch 'master' of ssh://git.debian.org/git/debian-med/barrnap new d453a3a bump Standards-Version The 6 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. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/barrnap.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
