[pypy-issue] Issue #2908: Segfault when reading a GraphViz file with Pygraphviz (pypy/pypy)
New issue 2908: Segfault when reading a GraphViz file with Pygraphviz https://bitbucket.org/pypy/pypy/issues/2908/segfault-when-reading-a-graphviz-file-with Shaun Jackman: I installed Pypy3 6.0.0 and GraphViz 2.40.1 using Linuxbrew `brew install pypy3 graphviz`, and I installed Pygraphviz 1.5 and Networkx 2.2 using `pip_pypy3 install --user pygraphviz networkx`. When I attempt to write a GraphViz file using `networkx.write_dot`, it segafults in `_IO_new_fdopen iofdopen.c:63` called by `_wrap_agwrite` in `_graphviz.pypy3-60-x86_64-linux-gnu.so`. It appears to be dereferencing a null pointer. Here's the backtrace: ``` (gdb) bt #0 _IO_new_fdopen (fd=1, mode=0x0) at iofdopen.c:63 #1 0x7fc0ef4fb759 in _wrap_agwrite () from /home/sjackman/.local/lib/python3.5/site-packages/pygraphviz/_graphviz.pypy3-60-x86_64-linux-gnu.so #2 0x7fc0ed183984 in ?? () from /gsc/btl/linuxbrew/Cellar/pypy3/6.0.0/lib/libpypy3-c.so (gdb) x/i $pc => 0x7fc0eb9a67b <_IO_new_fdopen+11>: movzbl (%rsi),%eax (gdb) p/x $rsi $1 = 0x0 ``` This works as expected when using CPython 3.7.0 rather than Pypy3. For my purpose, I have found Pypy3 to be four times faster than CPython. Any thoughts on how to troubleshoot this issue? See also https://github.com/pygraphviz/pygraphviz/issues/177 ___ pypy-issue mailing list pypy-issue@python.org https://mail.python.org/mailman/listinfo/pypy-issue
[jira] [Commented] (SPARK-18778) Fix the Scala classpath in the spark-shell
[
https://issues.apache.org/jira/browse/SPARK-18778?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16368442#comment-16368442
]
Shaun Jackman commented on SPARK-18778:
---
I have this issue as well. spark-shell fails with Java 9. Is there a work
around?
{{❯❯❯ spark-shell 'sc.parallelize(1 to 1000).count()'}}{{Failed to initialize
compiler: object java.lang.Object in compiler mirror not found.}}{{** Note that
as of 2.8 scala does not assume use of the java classpath.}}{{** For the old
behavior pass -usejavacp to scala, or if using a Settings}}{{** object
programmatically, settings.usejavacp.value = true.}}
> Fix the Scala classpath in the spark-shell
> --
>
> Key: SPARK-18778
> URL: https://issues.apache.org/jira/browse/SPARK-18778
> Project: Spark
> Issue Type: Improvement
> Components: Spark Core
>Affects Versions: 1.6.1, 2.0.2
>Reporter: DjvuLee
>Priority: Major
>
> Failed to initialize compiler: object scala.runtime in compiler mirror not
> found.
> ** Note that as of 2.8 scala does not assume use of the java classpath.
> ** For the old behavior pass -usejavacp to scala, or if using a Settings
> ** object programatically, settings.usejavacp.value = true.
> Exception in thread "main" java.lang.AssertionError: assertion failed: null
> at scala.Predef$.assert(Predef.scala:179)
> at
> org.apache.spark.repl.SparkIMain.initializeSynchronous(SparkIMain.scala:247)
> at
> org.apache.spark.repl.SparkILoop$$anonfun$org$apache$spark$repl$SparkILoop$$process$1.apply$mcZ$sp(SparkILoop.scala:990)
> at
> org.apache.spark.repl.SparkILoop$$anonfun$org$apache$spark$repl$SparkILoop$$process$1.apply(SparkILoop.scala:945)
> at
> org.apache.spark.repl.SparkILoop$$anonfun$org$apache$spark$repl$SparkILoop$$process$1.apply(SparkILoop.scala:945)
> at
> scala.tools.nsc.util.ScalaClassLoader$.savingContextLoader(ScalaClassLoader.scala:135)
> at
> org.apache.spark.repl.SparkILoop.org$apache$spark$repl$SparkILoop$$process(SparkILoop.scala:945)
> at org.apache.spark.repl.SparkILoop.process(SparkILoop.scala:1059)
> at org.apache.spark.repl.Main$.main(Main.scala:31)
> at org.apache.spark.repl.Main.main(Main.scala)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:498)
> at
> org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:731)
> at
> org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:181)
> at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:206)
> at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:121)
> at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
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[jira] [Comment Edited] (SPARK-18778) Fix the Scala classpath in the spark-shell
[
https://issues.apache.org/jira/browse/SPARK-18778?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel=16368442#comment-16368442
]
Shaun Jackman edited comment on SPARK-18778 at 2/18/18 5:25 AM:
I have this issue as well. spark-shell fails with Java 9. Is there a work
around?
{{❯❯❯ spark-shell 'sc.parallelize(1 to 1000).count()'}}
{{Failed to initialize compiler: object java.lang.Object in compiler mirror not
found.}}{{** Note that as of 2.8 scala does not assume use of the java
classpath.}}{{** For the old behavior pass -usejavacp to scala, or if using a
Settings}}{{** object programmatically, settings.usejavacp.value = true.}}
was (Author: sjackman):
I have this issue as well. spark-shell fails with Java 9. Is there a work
around?
{{❯❯❯ spark-shell 'sc.parallelize(1 to 1000).count()'}}{{Failed to initialize
compiler: object java.lang.Object in compiler mirror not found.}}{{** Note that
as of 2.8 scala does not assume use of the java classpath.}}{{** For the old
behavior pass -usejavacp to scala, or if using a Settings}}{{** object
programmatically, settings.usejavacp.value = true.}}
> Fix the Scala classpath in the spark-shell
> --
>
> Key: SPARK-18778
> URL: https://issues.apache.org/jira/browse/SPARK-18778
> Project: Spark
> Issue Type: Improvement
> Components: Spark Core
>Affects Versions: 1.6.1, 2.0.2
>Reporter: DjvuLee
>Priority: Major
>
> Failed to initialize compiler: object scala.runtime in compiler mirror not
> found.
> ** Note that as of 2.8 scala does not assume use of the java classpath.
> ** For the old behavior pass -usejavacp to scala, or if using a Settings
> ** object programatically, settings.usejavacp.value = true.
> Exception in thread "main" java.lang.AssertionError: assertion failed: null
> at scala.Predef$.assert(Predef.scala:179)
> at
> org.apache.spark.repl.SparkIMain.initializeSynchronous(SparkIMain.scala:247)
> at
> org.apache.spark.repl.SparkILoop$$anonfun$org$apache$spark$repl$SparkILoop$$process$1.apply$mcZ$sp(SparkILoop.scala:990)
> at
> org.apache.spark.repl.SparkILoop$$anonfun$org$apache$spark$repl$SparkILoop$$process$1.apply(SparkILoop.scala:945)
> at
> org.apache.spark.repl.SparkILoop$$anonfun$org$apache$spark$repl$SparkILoop$$process$1.apply(SparkILoop.scala:945)
> at
> scala.tools.nsc.util.ScalaClassLoader$.savingContextLoader(ScalaClassLoader.scala:135)
> at
> org.apache.spark.repl.SparkILoop.org$apache$spark$repl$SparkILoop$$process(SparkILoop.scala:945)
> at org.apache.spark.repl.SparkILoop.process(SparkILoop.scala:1059)
> at org.apache.spark.repl.Main$.main(Main.scala:31)
> at org.apache.spark.repl.Main.main(Main.scala)
> at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:498)
> at
> org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:731)
> at
> org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:181)
> at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:206)
> at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:121)
> at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
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Make and Clusters
Hi, David. Two options: 1. Use Biomake, which is mostly compatible with GNU Make, and supports submitting jobs to Slurm. https://github.com/evoldoers/biomake It can be installed with Linuxbrew on Linux or Homebrew on macOS. brew install homebrew/science/biomake 2. Precede each command that you want to run on the cluster with $qsub. Set that variable qsub to submit a job and wait for it to finish. For example: # Slurm qsub=sbatch --wait # SGE qsub=qsub -sync y # PBS qsub=qsub -Wblock=true I haven't tried but it seems possible that you could set the variables SHELL and .SHELLFLAGS to run qsub for every command. See https://www.gnu.org/software/make/manual/html_node/Choosing-the-Shell.html Cheers, Shaun ___ Help-make mailing list Help-make@gnu.org https://lists.gnu.org/mailman/listinfo/help-make
Re: FYI: New Abyss 2.0 contains undistributable components
Hi, Andreas. ABySS 2.0.1 is now GPL-3 without the non-commercial restriction! https://github.com/bcgsc/abyss/releases Cheers, Shaun -- http://sjackman.ca On September 6, 2016 at 09:13:44, Andreas Tille (andr...@an3as.eu) wrote: Hi Shaun, On Tue, Sep 06, 2016 at 03:49:16PM +, Shaun Jackman wrote: > Hi, Andreas. All of the code in ABySS to which I hold copyright is GPL > without restriction. Good. :-) > I'm not the sole copyright holder of ABySS. The BC > Cancer Agency holds much of the copyright. The best I can do is to make a > recommendation to the technology transfer office lawyer. I'll write the > e-mail, and we'll see how it goes. This would be great. We are currently trying to free several pieces of software and having a free ABySS would be complete this set. Thanks for trying Andreas. -- http://fam-tille.de
Re: FYI: New Abyss 2.0 contains undistributable components
Hi, Andreas. All of the code in ABySS to which I hold copyright is GPL without restriction. I'm not the sole copyright holder of ABySS. The BC Cancer Agency holds much of the copyright. The best I can do is to make a recommendation to the technology transfer office lawyer. I'll write the e-mail, and we'll see how it goes. Cheers, Shaun On Tue, 6 Sep 2016 at 08:34 Andreas Tille <andr...@an3as.eu> wrote: > Hi Shaun, > > On Mon, Sep 05, 2016 at 01:50:57PM -0700, Shaun Jackman wrote: > > The license of ABySS 2.0 is unchanged from ABySS 1.9. The license of > ABySS > > and all of the files contained in https://github.com/bcgsc/abyss are > > described in https://github.com/bcgsc/abyss/blob/master/COPYRIGHT > > I vaguely remember that we discussed ABySS license in private mail but > I'd like to come back here on the list to make you consider giving up a > non-free license. Besides the fact that it would be better to drop the > non-commercial restriction at all I think a license saying > > You may use, redistribute and modify this software for non-commercial > purposes under the terms of the GNU General Public License > > The restriction you apply to GPL afterwards seems to contradict the > GPL idea IMHO. > > It would be great if you could reconsider to simply drop the restriction. > > Kind regards > > Andreas. > > -- > http://fam-tille.de > -- http://sjackman.ca
Re: git rebase -i without altering the committer date
On April 20, 2016 at 13:37:01, Junio C Hamano (gits...@pobox.com(mailto:gits...@pobox.com)) wrote: > Shaun Jackman writes: > > > I'd like to insert a commit between two commits without changing > > the committer date or author date of that commit or the subsequent > > commits. I'd planned on using `git rebase -i` to insert the > > commit. I believe it retains the author date, but changes the > > committer date to the current time. I've seen the options > > `--committer-date-is-author-date` and `--ignore-date`, but I don't > > believe either of those options does what I want. If no such > > option currently exists to leave the committer and author date > > unchanged, is there any chance that this functionality could > > please be implemented? > > You can mark the commit as "edit", use "git commit --amend" when > "rebase -i" stops and gives control back to you, and say "rebase > --continue". That way, you can use your favourite trick to lie > about committer date (or identity or other aspects) when running > "git commit --amend" and its effect will be left in the resulting > history, I would think. Thanks for the suggestion, Junio. That would retain the committer date for the commit being inserted. I believe that the subsequent commits would have their committer date modified to the current time by the `git rebase --continue`. Cheers, Shaun -- To unsubscribe from this list: send the line "unsubscribe git" in the body of a message to majord...@vger.kernel.org More majordomo info at http://vger.kernel.org/majordomo-info.html
git rebase -i without altering the committer date
I'd like to insert a commit between two commits without changing the committer date or author date of that commit or the subsequent commits. I'd planned on using `git rebase -i` to insert the commit. I believe it retains the author date, but changes the committer date to the current time. I've seen the options `--committer-date-is-author-date` and `--ignore-date`, but I don't believe either of those options does what I want. If no such option currently exists to leave the committer and author date unchanged, is there any chance that this functionality could please be implemented? For a relevant SO question, see How to make a git rebase and keep the commit timestamp? http://stackoverflow.com/questions/30790645/how-to-make-a-git-rebase-and-keep-the-commit-timestamp Thanks, Shaun -- http://sjackman.ca -- To unsubscribe from this list: send the line "unsubscribe git" in the body of a message to majord...@vger.kernel.org More majordomo info at http://vger.kernel.org/majordomo-info.html
[pcre-dev] [Bug 1525] New: RunTest fails with GCC 4.9.1
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You are on the CC list for the bug.
http://bugs.exim.org/show_bug.cgi?id=1525
Summary: RunTest fails with GCC 4.9.1
Product: PCRE
Version: 8.35
Platform: x86-64
URL: https://gist.github.com/0d8399572dc78e4ba349
OS/Version: Linux
Status: NEW
Severity: bug
Priority: medium
Component: Code
AssignedTo: p...@hermes.cam.ac.uk
ReportedBy: sjack...@gmail.com
CC: pcre-dev@exim.org
PCRE fails make check RunTest when compiled with GCC 4.9.1, but passes on the
same system when compiled with GCC 4.4.7.
Please see the following error message and the linked gist.
https://gist.github.com/0d8399572dc78e4ba349
Configuration
=
./configure --disable-dependency-tracking
--prefix=/home/sjackman/.linuxbrew/Cellar/pcre/8.35 --enable-utf8
--enable-pcre8 --enable-pcre16 --enable-pcre32 --enable-unicode-properties
--enable-pcregrep-libz --enable-pcregrep-libbz2 --enable-jit
GCC versions
=
$ gcc-4.4 --version
gcc-4.4 (GCC) 4.4.7 20120313 (Red Hat 4.4.7-1)
$ gcc-4.9 --version
gcc-4.9 (Homebrew gcc 4.9.1 --with-sysroot --without-multilib) 4.9.1
RunTest.log
PCRE C library tests using test data from ./testdata
PCRE version 8.35 2014-04-04
Testing 8-bit library
Test 1: Main functionality (Compatible with Perl = 5.10)
OK
OK with study
OK with JIT study
Test 2: API, errors, internals, and non-Perl stuff (not UTF-8)
--- ./testdata/testoutput2 2014-03-10 09:28:08.0 -0700
+++ testtry 2014-09-04 09:55:24.0 -0700
@@ -5821,13 +5821,16 @@
No match
/a{}/I
-Failed: number too big in {} quantifier at offset 22
+Capturing subpattern count = 0
+No options
+First char = 'a'
+No need char
/(){64294967295}/I
-Failed: number too big in {} quantifier at offset 14
+Failed: regular expression is too large at offset 15
/(){2,4294967295}/I
-Failed: number too big in {} quantifier at offset 15
+Failed: numbers out of order in {} quantifier at offset 15
(?i:a)(?i:b)(?i:c)(?i:d)(?i:e)(?i:f)(?i:g)(?i:h)(?i:i)(?i:j)(k)(?i:l)A\1BI
Capturing subpattern count = 1
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Bug#730902: avarice: diff for NMU version 2.11-1.1
Hi David, Thanks for fixing this bug in avarice. Please do go ahead with the NMU. avarice is up for adoption. See the RFA here: http://bugs.debian.org/732433 Would you like to adopt avarice? Cheers, Shaun -- http://sjackman.ca On 2013-Dec-22 at 10:39:11 , David Prévot (taf...@debian.org) wrote: tags 730902 + patch thanks Dear maintainer, I've prepared an NMU for avarice (versioned as 2.11-1.1) and uploaded it to DELAYED/2. Please feel free to tell me if I should delay it longer. Regards. David - avarice-2.11-1.1-nmu.diff, 921 bytes - signature.asc, 501 bytes
Bug#730902: avarice: diff for NMU version 2.11-1.1
Hi David, Thanks for fixing this bug in avarice. Please do go ahead with the NMU. avarice is up for adoption. See the RFA here: http://bugs.debian.org/732433 Would you like to adopt avarice? Cheers, Shaun -- http://sjackman.ca On 2013-Dec-22 at 10:39:11 , David Prévot (taf...@debian.org) wrote: tags 730902 + patch thanks Dear maintainer, I've prepared an NMU for avarice (versioned as 2.11-1.1) and uploaded it to DELAYED/2. Please feel free to tell me if I should delay it longer. Regards. David - avarice-2.11-1.1-nmu.diff, 921 bytes - signature.asc, 501 bytes
Bug#732430: RM: pptview -- RoM, no rdepends
Package: ftp.debian.org Severity: normal Hi, Please remove pptview. It's quite dated (circa 1997), and there are better free alternatives now. It has two open Ubuntu bugs. installation fails for amd64 https://bugs.launchpad.net/ubuntu/+source/pptview/+bug/909447 PowerPoint viewer version 97 can't open OpenXML PPSX presentations https://bugs.launchpad.net/ubuntu/+source/pptview/+bug/1242369 Thanks, Shaun -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#732431: RM: pocketpc-cab -- RoM, unmaintained upstream
Package: ftp.debian.org Severity: normal Hi, Please remove pocketpc-cab. I'm the upstream developer and the Debian package maintainer, and it hasn't been maintained in many years. Thanks, Shaun -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#732430: Fwd: Remove or Fix Debian‘s pptview
From: Ma Xiaojun damage3...@gmail.com Date: 17 December 2013 07:51 Subject: Remove or Fix Debian‘s pptview To: sjack...@debian.org Hi, pptview is actually a pretty smart work. It offers a high level of desktop integration, it somehow conforms to FHS, ... However, it also have multiple issues today. * The version is dated by today's standard: https://bugs.launchpad.net/ubuntu/+source/pptview/+bug/1242369 * Suggested openoffice.org-impress no longer exist * If there is a pptview, where is docview or xlsview? I guess the simplest resolution is simply remove it. So users won't be disappointed by it. If people want viewers from MSFT they should go for winetricks or CrossOver or whatever wine frontends. Regards, Ma Xiaojun -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#732433: RFA: avarice -- use GDB with Atmel's JTAG ICE for the AVR
Package: wnpp Please adopt avarice. A new upstream version is available: 2.13. http://avarice.sourceforge.net/ Thanks, Shaun -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#732433: RFA: avarice -- use GDB with Atmel's JTAG ICE for the AVR
Package: wnpp Please adopt avarice. A new upstream version is available: 2.13. http://avarice.sourceforge.net/ Thanks, Shaun -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/cadx6m3p+fawv4en-on+wpvozyhyuvhh-4o3_jj5vf+8yykg...@mail.gmail.com
Bug#702440: closed by Charles Plessy ple...@debian.org (Bug#702440: fixed in abyss 1.3.6-1)
Fantastic. Thanks for the GCC 4.8 patch. We'll merge it upstream. On 7 September 2013 20:21, Debian Bug Tracking System ow...@bugs.debian.org wrote: This is an automatic notification regarding your Bug report which was filed against the abyss package: #702440: New upstream release available It has been closed by Charles Plessy ple...@debian.org. Their explanation is attached below along with your original report. If this explanation is unsatisfactory and you have not received a better one in a separate message then please contact Charles Plessy ple...@debian.org by replying to this email. -- 702440: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=702440 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems -- Forwarded message -- From: Charles Plessy ple...@debian.org To: 702440-cl...@bugs.debian.org Cc: Date: Sun, 08 Sep 2013 03:18:19 + Subject: Bug#702440: fixed in abyss 1.3.6-1 Source: abyss Source-Version: 1.3.6-1 We believe that the bug you reported is fixed in the latest version of abyss, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 702...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Charles Plessy ple...@debian.org (supplier of updated abyss package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -BEGIN PGP SIGNED MESSAGE- Hash: SHA256 Format: 1.8 Date: Sun, 08 Sep 2013 11:36:44 +0900 Source: abyss Binary: abyss Architecture: source amd64 Version: 1.3.6-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org Changed-By: Charles Plessy ple...@debian.org Description: abyss - de novo, parallel, sequence assembler for short reads Closes: 702440 722072 Changes: abyss (1.3.6-1) unstable; urgency=low . * Team upload (Closes: #722072). e05ee57 Imported Upstream version 1.3.5 b391f1f Imported Upstream version 1.3.6 (Closes: #702440) 7edc28b Signal the use of git-buildpackage with this configuration file. a3beaac Normalised source package control file with config-model-edit. dd86394 Conforms with Policy version 3.9.4. 71d42ad Normalised VCS URLs. Checksums-Sha1: bf4e40f2c8b5257f9cf65487aa8e62df6e26cf03 2039 abyss_1.3.6-1.dsc ac5004972c90cedfb116b307dcf051fb30b7a102 678880 abyss_1.3.6.orig.tar.gz 672132adba821fb326a0d97905b9d2a090269053 11516 abyss_1.3.6-1.debian.tar.gz f1301a6d7f7f3ab961264c4e11d3058ad282381d 867230 abyss_1.3.6-1_amd64.deb Checksums-Sha256: 300b63319b5422eb5b46253135e8e8405e3ad39c5b1822d978f07be86a8985ff 2039 abyss_1.3.6-1.dsc 4432a8b5046bdcb548b6f1b22069a6cade4dea26fc6f83ad5467548e4f3e7c95 678880 abyss_1.3.6.orig.tar.gz 8246ebd6c9ba9539ddad05450f7be0bbab5dd6cdb0d8dff2f7a5f54b136b2139 11516 abyss_1.3.6-1.debian.tar.gz 921ca17052122d1aa45bd5c732fd8d14508f88fde8db4ef2c0b6cf624a449938 867230 abyss_1.3.6-1_amd64.deb Files: 2f8a23a6373dcee6b6d1cd02b7a40478 2039 non-free/science optional abyss_1.3.6-1.dsc 4182c24de5b74a1294fc8f9a452ae743 678880 non-free/science optional abyss_1.3.6.orig.tar.gz cdf33bfd6ae35dc2482c46545ebdbb4b 11516 non-free/science optional abyss_1.3.6-1.debian.tar.gz ee386cc32f08ec888b10f7430ed09565 867230 non-free/science optional abyss_1.3.6-1_amd64.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.14 (GNU/Linux) iQIcBAEBCAAGBQJSK+tXAAoJEMW9bI8ildUCu7MP/imSl48hRDCNs4AEB1ObGa5g 7tULd1qRSBsnGIj1xe/RVAslyadsomDOK6huljomZndIPyYq7nAldaV+RPy+GVeI JqjoIh5HmkUzpRVZkUtPKG0LdDsUQ5GMPBjnUGwjP9EjhK/j6c+9IPoDBPaxoMtP U+O9K+o/SgqiEtYtAdIZN0ISEJUYmAN+v3X65Eiozq25GgA/4uOe1qqWgzOcMtOP poK/ujqcZNFtWMwxzKtdx+CDO8CLVtgBDXoRFtfXgqPyW9uUmzMG1Gg++IrozZMU 7CCxUmg2j7B1IjOoKtkRe0Eo8yjrFxoCqK2NdyMUmNJGpZxM0tgzjjYufbJqbSsD pbjQ+GeU1TGi3v2+SZx1TDaE+VKURiIIM/P9uT5jHuyBuQpW8uXwfiu77lqiE8K0 Yy6FXS//ZRiwa5WYwGGv7ca9rhsEmJxZJjoHvLJDKN2fOHer38A51jxxur4hrSqt wkQCfJXyp9WECl/O6ZFLJ3+T8IT8KyYiuQM+9FCTcXoYX3ESq4R9Md+UZyhCx5Ck ob5MOGb4MYhKpryZCPsLYDm208UU1wDyKLDduiue82t4Eo/fVYZT85B7f/E7lLpf VcdEIHjgSQREXKqOL68RaEryrxWVFXat16yEurUjbcvGhW1Lyb5m9V7osIBlxiXF nBcrfEdC/q4CuHGBL8MP =+D8f -END PGP SIGNATURE- -- Forwarded message -- From: Shaun Jackman sjack...@gmail.com To: Submit@BTS sub...@bugs.debian.org Cc: Date: Wed, 6 Mar 2013 07:50:30 -0800 Subject: New upstream release available Package: abyss Priority: wishlist ABySS 1.3.5 is available. Cheers, Shaun -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas
Bug#702440: New upstream release available
Hi Andreas, My home machine is running OS X and I use Homebrew to manage packages, and at work I don't have root access on the Linux servers, so I use Linuxbrew to manage packages. To maintain a Debian package, there's a little extra effort required to fire up a VM. I opened the bug report to document that a new version of ABySS is available. If you have time to update the package, that's great, otherwise it'll wait until I find some time to do it. Thanks for the bug report. It's an easy one line fix (delete the offending line) and will definitely be included in the next release of ABySS. Here's a link to the upstream bug report. https://github.com/bcgsc/abyss/issues/26 Cheers, Shaun — http://about.me/sjackman On Wed, Aug 14, 2013 at 4:58 PM, Andreas Tille andr...@fam-tille.de wrote: Hi Shaun, I wonder if there is any reason that you did just files a bug report about a new version and did not simply uploaded the package as you formerly did. Could you please drop the Debian Med team some note if something prevents you from doing so. BTW, I checked the latest version and injected it into the Git repository but I realised that it does not build because of: g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I. -I/usr/lib/openmpi/include -D_FORTIFY_SOURCE=2 -Wall -Wextra -Werror -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -c -o libassembly_a-DotWriter.o `test -f 'DotWriter.cpp' || echo './'`DotWriter.cpp In file included from DotWriter.cpp:5:0: ../Graph/ContigGraphAlgorithms.h: In function 'OutIt assemble_if(Graph, OutIt, Predicate)': ../Graph/ContigGraphAlgorithms.h:202:44: error: typedef 'vertex_descriptor' locally defined but not used [-Werror=unused-local-typedefs] typedef typename Graph::vertex_descriptor vertex_descriptor; ^ cc1plus: all warnings being treated as errors make[3]: *** [libassembly_a-DotWriter.o] Error 1 make[3]: Leaving directory `/tmp/buildd/abyss-1.3.6/Assembly' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/tmp/buildd/abyss-1.3.6' make[1]: *** [all] Error 2 make[1]: Leaving directory `/tmp/buildd/abyss-1.3.6' dh_auto_build: make -j1 returned exit code 2 Since you are upstream dealing with things like this would be way simpler if you just fix these things upstream rather than leaving us poor packagers alone with patching. Kind regards Andras. -- http://fam-tille.de
[R] Convert rbind of lists to data.frame
I'm trying to build a data.frame row-by-row like so:
df - data.frame(rbind(list('a',1), list('b', 2), list('c', 3)))
I was surprised to see that the columns of the resulting data.frame
are stored in lists rather than vectors.
str(df)
'data.frame': 3 obs. of 2 variables:
$ X1:List of 3
..$ : chr a
..$ : chr b
..$ : chr c
$ X2:List of 3
..$ : num 1
..$ : num 2
..$ : num 3
The desired result is:
str(df)
'data.frame': 3 obs. of 2 variables:
$ X1: chr a b c
$ X2: num 1 2 3
The following works, but is rather ugly:
df - data.frame(lapply(data.frame(rbind(list('a',1), list('b', 2),
list('c', 3))), unlist))
Thanks,
Shaun
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Lattice barchart with error bars
Hi Bert, Dennis, I'll agree that using a barchart was a poor choice. I was in fact using a notched bwplot to show the median and confidence interval of the median. In this case it's the median and confidence interval that I want to highlight, and I find that the visual noise of the box and whiskers is detracting from the focus, and those wee notches are not much to focus on. So, I'd like to draw a stripplot with error bars, preferably in Lattice. Let's call this a TIE fighter plot. Any suggestions? Cheers, Shaun On 4 July 2013 18:00, Dennis Murphy djmu...@gmail.com wrote: If you consult the lattice package help, you'll discover there is no panel_errorbar() function, which would imply the package developers have a distaste for that type of graphic. If you fish around the R-help archives, though, you might be able to find someone who wrote a function to do error bars in lattice. (Use a searchable archive such as Nabble to hunt for it.) Error bar plots are easier to do in the ggplot2 package, since there is a specific function to generate the error bar 'geometry' (geom_errorbar). See http://docs.ggplot2.org/current/ for an expanded version of the package help pages, which include the graphs generated by the code. I believe there's also a base graphics version that you can get from the gplots package, but I don't know a lot about it. Dennis On Thu, Jul 4, 2013 at 2:53 PM, Shaun Jackman sjack...@gmail.com wrote: Hi, I'd like to draw a lattice barchart of means with error bars to show the standard deviation. I have the barchart, how do I add the error bars? require(datasets) require(lattice) x - aggregate(weight ~ Diet, ChickWeight, function(x) c(mean=mean(x), sd=sd(x))) barchart(weight[,'mean'] ~ Diet, x) Thanks, Shaun __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Lattice barchart with error bars
Yes! Thank you, David. That's exactly what I'm I'm looking for. For the record, here's a couple pages leading to this answer: http://www.hep.by/gnu/r-patched/r-faq/R-FAQ_89.html http://latticeextra.r-forge.r-project.org/man/segplot.html http://rgm3.lab.nig.ac.jp/RGM/r_function?p=latticeExtraf=segplot For a related question, what's the tidiest way to calculate the medians and confidence intervals? Currently I'm using `boxplot`: require(datasets) ci - with(boxplot(weight ~ Diet, ChickWeight), data.frame( Diet = names, median = stats[3,], lower = conf[1,], upper = conf[2,])) Cheers, Shaun On 5 July 2013 11:28, David Winsemius dwinsem...@comcast.net wrote: On Jul 5, 2013, at 11:15 AM, Shaun Jackman wrote: Hi Bert, Dennis, I'll agree that using a barchart was a poor choice. I was in fact using a notched bwplot to show the median and confidence interval of the median. In this case it's the median and confidence interval that I want to highlight, and I find that the visual noise of the box and whiskers is detracting from the focus, and those wee notches are not much to focus on. So, I'd like to draw a stripplot with error bars, preferably in Lattice. Let's call this a TIE fighter plot. Any suggestions? I like the TIE fighter label. Try this: library(latticeExtra) data(USCancerRates) segplot(reorder(factor(county), rate.male) ~ LCL95.male + UCL95.male, data = subset(USCancerRates, state == Washington), draw.bands = FALSE, centers = rate.male, segments.fun = panel.arrows, ends = both, angle = 90, length = 1, unit = mm) It's what Sarkar has recommended in the past when this request has been posted. -- David Cheers, Shaun On 4 July 2013 18:00, Dennis Murphy djmu...@gmail.com wrote: If you consult the lattice package help, you'll discover there is no panel_errorbar() function, which would imply the package developers have a distaste for that type of graphic. If you fish around the R-help archives, though, you might be able to find someone who wrote a function to do error bars in lattice. (Use a searchable archive such as Nabble to hunt for it.) Error bar plots are easier to do in the ggplot2 package, since there is a specific function to generate the error bar 'geometry' (geom_errorbar). See http://docs.ggplot2.org/current/ for an expanded version of the package help pages, which include the graphs generated by the code. I believe there's also a base graphics version that you can get from the gplots package, but I don't know a lot about it. Dennis On Thu, Jul 4, 2013 at 2:53 PM, Shaun Jackman sjack...@gmail.com wrote: Hi, I'd like to draw a lattice barchart of means with error bars to show the standard deviation. I have the barchart, how do I add the error bars? require(datasets) require(lattice) x - aggregate(weight ~ Diet, ChickWeight, function(x) c(mean=mean(x), sd=sd(x))) barchart(weight[,'mean'] ~ Diet, x) Thanks, Shaun __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Lattice barchart with error bars
Hmm. Interesting point, Bert. I don't know whether the notches show the 95% confidence interval or the median, or the 95% confidence interval that two non-overlapping notches have different medians. You're saying it's the latter? Anyone know what the 95% confidence interval of the median would be? Cheers, Shaun The notches (if requested) extend to +/-1.58 IQR/sqrt(n). This seems to be based on the same calculations as the formula with 1.57 in Chambers et al. (1983, p. 62), given in McGill et al. (1978, p. 16). They are based on asymptotic normality of the median and roughly equal sample sizes for the two medians being compared, and are said to be rather insensitive to the underlying distributions of the samples. The idea appears to be to give roughly a 95% confidence interval for the difference in two medians. On 5 July 2013 11:48, Bert Gunter gunter.ber...@gene.com wrote: Be careful! You are talking about 2 different varieties of apples here. As I read it, the CI's in the cancer data, which I know is just for example purposes, are CI's for the **individual means**; the notches in boxplots are nonparametric and for 2 groups with roughly equal sample sizes, The idea appears to be to give roughly a 95% confidence interval for the **difference** in two medians. (from ?boxplot.stats). So I'm not sure which you want, but they are certainly different (by a factor of around sqrt(2),right?), even if both are for the mean or both are for the median. Cheers, Bert On Fri, Jul 5, 2013 at 11:28 AM, David Winsemius dwinsem...@comcast.net wrote: On Jul 5, 2013, at 11:15 AM, Shaun Jackman wrote: Hi Bert, Dennis, I'll agree that using a barchart was a poor choice. I was in fact using a notched bwplot to show the median and confidence interval of the median. In this case it's the median and confidence interval that I want to highlight, and I find that the visual noise of the box and whiskers is detracting from the focus, and those wee notches are not much to focus on. So, I'd like to draw a stripplot with error bars, preferably in Lattice. Let's call this a TIE fighter plot. Any suggestions? I like the TIE fighter label. Try this: library(latticeExtra) data(USCancerRates) segplot(reorder(factor(county), rate.male) ~ LCL95.male + UCL95.male, data = subset(USCancerRates, state == Washington), draw.bands = FALSE, centers = rate.male, segments.fun = panel.arrows, ends = both, angle = 90, length = 1, unit = mm) It's what Sarkar has recommended in the past when this request has been posted. -- David Cheers, Shaun On 4 July 2013 18:00, Dennis Murphy djmu...@gmail.com wrote: If you consult the lattice package help, you'll discover there is no panel_errorbar() function, which would imply the package developers have a distaste for that type of graphic. If you fish around the R-help archives, though, you might be able to find someone who wrote a function to do error bars in lattice. (Use a searchable archive such as Nabble to hunt for it.) Error bar plots are easier to do in the ggplot2 package, since there is a specific function to generate the error bar 'geometry' (geom_errorbar). See http://docs.ggplot2.org/current/ for an expanded version of the package help pages, which include the graphs generated by the code. I believe there's also a base graphics version that you can get from the gplots package, but I don't know a lot about it. Dennis On Thu, Jul 4, 2013 at 2:53 PM, Shaun Jackman sjack...@gmail.com wrote: Hi, I'd like to draw a lattice barchart of means with error bars to show the standard deviation. I have the barchart, how do I add the error bars? require(datasets) require(lattice) x - aggregate(weight ~ Diet, ChickWeight, function(x) c(mean=mean(x), sd=sd(x))) barchart(weight[,'mean'] ~ Diet, x) Thanks, Shaun __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius Alameda, CA, USA -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained
[R] Lattice barchart with error bars
Hi, I'd like to draw a lattice barchart of means with error bars to show the standard deviation. I have the barchart, how do I add the error bars? require(datasets) require(lattice) x - aggregate(weight ~ Diet, ChickWeight, function(x) c(mean=mean(x), sd=sd(x))) barchart(weight[,'mean'] ~ Diet, x) Thanks, Shaun __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Comparing each level of a factor to the global mean
Hi Jean, contr.treatment(4) shows what the default contrast matrix looks like for a factor with 4 levels. What function do I use to create a contrast matrix to compare each level with the global mean (four comparisons in total), and produce a table similar to `summary.lm`? Thanks, Shaun On 26 June 2013 05:50, Adams, Jean jvad...@usgs.gov wrote: Shaun, See the help on contrasts ... ?contr.treatment Jean On Tue, Jun 25, 2013 at 7:07 PM, Shaun Jackman sjack...@gmail.com wrote: Hi, I've used `lm` to create a linear model of a continuous variable against a factor variable with four levels using an example R data set (see below). By default, it uses a treatment contrast matrix that compares each level of the factor variable with the first reference level (three comparisons in total). I'd like to compare each level with the global mean (four comparisons in total), and produce a table similar to `summary.lm`. How do I go about this? ```r model - lm(weight ~ Diet, ChickWeight) summary(model) ``` Thanks, Shaun __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Comparing each level of a factor to the global mean
Hi, I've used `lm` to create a linear model of a continuous variable against a factor variable with four levels using an example R data set (see below). By default, it uses a treatment contrast matrix that compares each level of the factor variable with the first reference level (three comparisons in total). I'd like to compare each level with the global mean (four comparisons in total), and produce a table similar to `summary.lm`. How do I go about this? ```r model - lm(weight ~ Diet, ChickWeight) summary(model) ``` Thanks, Shaun __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Bug#702440: New upstream release available
Package: abyss Priority: wishlist ABySS 1.3.5 is available. Cheers, Shaun
Re: [Haskell-cafe] ByteString.getContents fails for files 2GB on OS X
System.IO.MMap (mmapFileByteString) worked like a charm in loading files larger than 2 GB on OS X. Using mmapFileByteString and strict ByteString is roughly seven times faster for my program than using getContents and ByteString.Lazy. Cheers, Shaun On 11 June 2012 07:08, Gracjan Polak gracjanpo...@gmail.com wrote: Gregory Collins greg at gregorycollins.net writes: Try http://hackage.haskell.org/package/bytestring-mmap ? Or: http://hackage.haskell.org/package/mmap -- Gracjan ___ Haskell-Cafe mailing list Haskell-Cafe@haskell.org http://www.haskell.org/mailman/listinfo/haskell-cafe ___ Haskell-Cafe mailing list Haskell-Cafe@haskell.org http://www.haskell.org/mailman/listinfo/haskell-cafe
Accepted gmap 2012-06-12-1 (source amd64)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Tue, 12 Jun 2012 15:06:22 -0700 Source: gmap Binary: gmap Architecture: source amd64 Version: 2012-06-12-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: gmap - spliced and SNP-tolerant alignment for mRNA and short reads Changes: gmap (2012-06-12-1) unstable; urgency=low . * New upstream release Checksums-Sha1: 38c84f66c8d136e9845eb1e40edb98c1f1096509 1300 gmap_2012-06-12-1.dsc 592167d00e62e636cb52acb1aa2b6a5b8c9d2d4a 3618172 gmap_2012-06-12.orig.tar.gz 1bb8d0e864d44393c38ad9597e1f479735e7f46e 13014 gmap_2012-06-12-1.debian.tar.gz fa9cd7d7374baa8d02c710a250ed1aecf2d75d79 7799184 gmap_2012-06-12-1_amd64.deb Checksums-Sha256: 3a1b8410781c6c838f03ef2c7abdadf9981c23a615ad56ec44f9bb4c3a311037 1300 gmap_2012-06-12-1.dsc 797bd925cc5fc40cf4849db7f1cf0b016cc114678cdfb6cdf93066c86b3c037e 3618172 gmap_2012-06-12.orig.tar.gz 830cf6e33c19ccfce22e2370319ce3343403740117852d9aeb30d10986c1d414 13014 gmap_2012-06-12-1.debian.tar.gz 88e1b25f6fb19ab11719af11d2a1fdcf17f8a0070f40071e8566d55de4223d50 7799184 gmap_2012-06-12-1_amd64.deb Files: a8710a05fdbd10a1f45419a5083fa60f 1300 non-free/science optional gmap_2012-06-12-1.dsc bf4a663415d09bb55e12989637155e36 3618172 non-free/science optional gmap_2012-06-12.orig.tar.gz b967a6ef5b0ffd8bc9e67f70ffc4ad9c 13014 non-free/science optional gmap_2012-06-12-1.debian.tar.gz c4843968230b179fcc2d1557d2cf530a 7799184 non-free/science optional gmap_2012-06-12-1_amd64.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAk/XwqgACgkQvFdYF1IwUUrOnQCgpiM4HHe4ygpmz0phs32IQSnY 1EwAoO94GLTmCxr5CIu/ySOC6VU1xWal =H9q/ -END PGP SIGNATURE- Accepted: gmap_2012-06-12-1.debian.tar.gz to non-free/g/gmap/gmap_2012-06-12-1.debian.tar.gz gmap_2012-06-12-1.dsc to non-free/g/gmap/gmap_2012-06-12-1.dsc gmap_2012-06-12-1_amd64.deb to non-free/g/gmap/gmap_2012-06-12-1_amd64.deb gmap_2012-06-12.orig.tar.gz to non-free/g/gmap/gmap_2012-06-12.orig.tar.gz -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1sezso-0001gq...@franck.debian.org
Re: [Haskell-cafe] ByteString.getContents fails for files 2GB on OS X
Hi Erik, Serge, I have a 64-bit build of GHC: http://www.haskell.org/ghc/dist/7.4.1/ghc-7.4.1-x86_64-apple-darwin.tar.bz2 I think it's fundamentally an OS X issue. The system call read(2) fails for reads 2 GB with EINVAL, even though I have a 64-bit OS X kernel. GHC would need to hack around this issue. Cheers, Shaun On 8 June 2012 05:08, Serge Le Huitouze serge.lehuito...@gmail.com wrote: Isn't it more likely to be due to the garbage collector's strategy (copying) ? --Serge On Fri, Jun 8, 2012 at 10:29 AM, Erik Hesselink hessel...@gmail.com wrote: Do you have a 32bit or 64bit GHC build? That might have something to do with it, if you're nearing 2^32 (or 2^31) bytes. Erik On Fri, Jun 8, 2012 at 2:25 AM, Shaun Jackman sjack...@gmail.com wrote: Hi, Data.ByteString.Char8.getContents fails for files 2GB on OS X. Is there a fix for this? $ cat getContents.hs main = getContents $ ./getContents smallFile $ ./getContents bigFile getContents: stdin: hGetBuf: invalid argument (Invalid argument) $ ghc --version The Glorious Glasgow Haskell Compilation System, version 7.4.1 Mac OS X 10.7.4 64-bit As a workaround, I used ByteString.Lazy instead of the strict ByteString, which worked, but found it was ~4 times slower for my program, so I'd like to get the strict ByteString working with large files. Cheers, Shaun ___ Haskell-Cafe mailing list Haskell-Cafe@haskell.org http://www.haskell.org/mailman/listinfo/haskell-cafe ___ Haskell-Cafe mailing list Haskell-Cafe@haskell.org http://www.haskell.org/mailman/listinfo/haskell-cafe ___ Haskell-Cafe mailing list Haskell-Cafe@haskell.org http://www.haskell.org/mailman/listinfo/haskell-cafe
[Haskell-cafe] ByteString.getContents fails for files 2GB on OS X
Hi, Data.ByteString.Char8.getContents fails for files 2GB on OS X. Is there a fix for this? $ cat getContents.hs main = getContents $ ./getContents smallFile $ ./getContents bigFile getContents: stdin: hGetBuf: invalid argument (Invalid argument) $ ghc --version The Glorious Glasgow Haskell Compilation System, version 7.4.1 Mac OS X 10.7.4 64-bit As a workaround, I used ByteString.Lazy instead of the strict ByteString, which worked, but found it was ~4 times slower for my program, so I'd like to get the strict ByteString working with large files. Cheers, Shaun ___ Haskell-Cafe mailing list Haskell-Cafe@haskell.org http://www.haskell.org/mailman/listinfo/haskell-cafe
Accepted abyss 1.3.4-1 (source amd64)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Thu, 31 May 2012 11:39:13 -0700 Source: abyss Binary: abyss Architecture: source amd64 Version: 1.3.4-1 Distribution: unstable Urgency: low Maintainer: Shaun Jackman sjack...@debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: abyss - de novo, parallel, sequence assembler for short reads Changes: abyss (1.3.4-1) unstable; urgency=low . * New upstream release. * debian/copyright: Add CityHash, which has an Expat license. * debian/control: Bump Standards-Version to 3.9.3.1. Checksums-Sha1: 630aaf70e8ea9b5dd6703e9e15f2434d66c88adc 1109 abyss_1.3.4-1.dsc 763dc423054421829011844ceaa5e18dc43f1ca9 640545 abyss_1.3.4.orig.tar.gz 1377ea68655093152b2d3382b8f36ac59d01050e 9153 abyss_1.3.4-1.debian.tar.gz d07a77f4049c5020e0c41c65b52b1ff263f4ee4f 1721960 abyss_1.3.4-1_amd64.deb Checksums-Sha256: 3ce309039526a1917c9af1ee4cdbb452b9ada929bfc85910fc212d433c8d9e36 1109 abyss_1.3.4-1.dsc 6b6ccb04baaa9d244dd67d95e1512a934d2e54fd28a539149b6845ed5c496baf 640545 abyss_1.3.4.orig.tar.gz 03af5dc38d5c1d446fdaff03a165d8cae14e2a3b695d3beb17fd59352c24f402 9153 abyss_1.3.4-1.debian.tar.gz 2f3c5b7d3f47597ea675926952f177ec187c8f1c5c927b55768ddc230246283a 1721960 abyss_1.3.4-1_amd64.deb Files: 100d3e0498535e1c4103932c291de97e 1109 non-free/science optional abyss_1.3.4-1.dsc 5a79f33f828db3c626627c5facd0f712 640545 non-free/science optional abyss_1.3.4.orig.tar.gz df76ddfd14c3f3c122cb3e5106c2fafe 9153 non-free/science optional abyss_1.3.4-1.debian.tar.gz 64f7c4c94842802c2bed7edf9621046f 1721960 non-free/science optional abyss_1.3.4-1_amd64.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAk/HvUgACgkQvFdYF1IwUUqjJACg6aRlIIG2386yHIq2OPkJBZpG EWUAnj6asTEsiKGU5cG2ifsxO0xmwLkI =8EY2 -END PGP SIGNATURE- Accepted: abyss_1.3.4-1.debian.tar.gz to non-free/a/abyss/abyss_1.3.4-1.debian.tar.gz abyss_1.3.4-1.dsc to non-free/a/abyss/abyss_1.3.4-1.dsc abyss_1.3.4-1_amd64.deb to non-free/a/abyss/abyss_1.3.4-1_amd64.deb abyss_1.3.4.orig.tar.gz to non-free/a/abyss/abyss_1.3.4.orig.tar.gz -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1sadd4-0007aq...@franck.debian.org
Re: Patch for PLink to build using gcc-4.7 - please confirm that it is correct
Hi Andreas, I'd suggest using a scoped for loop rather than the original while loop. Cheers, Shaun On 2012-04-23, at 1:30 AM, Andreas Tille wrote: Hi Shaun, as you know the Debian Med team has packaged plink for Debian. Recently we received a bug report that the package does not build when using gcc 4.7 and we were working on a patch to solve this. You can find the patch here: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/plink/trunk/debian/patches/gcc-4.7.patch?view=markup I found this solution by the help of some people on debian-mentors list but I want to issue a BIG WARNING: If you look at the patch at the given URL in line 67 I admit I was just wild guessing what j you are really meaning. To my understanding this is very bad coding style and I would strongly recommend to strictly use different variables. I would be really happy if you would confirm that my wild guess was right (or please correct me if I was wrong) because my C coding knowledge is restricted to pure ANSII C and C++ looks sometimes quite magical to me. BTW, people at debian-mentors criticised the amount of warnings when using the -Wall option which unreveals a real lot of warnings which are hard to parse and some more strict following of coding guidelines might help here. Kind regards and thanks for providing plink as Free Software Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120423083050.gh16...@an3as.eu -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/711c5d11-81c5-4d6d-a2bb-38a90b776...@gmail.com
Re: Patch for PLink to build using gcc-4.7 - please confirm that it is correct
No worries, Andreas. It's just a coding style suggestion. Your solution is perfectly fine. Cheers, Shaun On 23 April 2012 11:48, Andreas Tille ti...@debian.org wrote: Hi Shaun, On Mon, Apr 23, 2012 at 08:43:22AM -0700, Shaun Jackman wrote: I'd suggest using a scoped for loop rather than the original while loop. Hi guess for a C++ programmer this hint is perfectly simple to implement however, for me this does not ring a bell without a patch. Thanks for the hint anyway - perhaps upstream will follow Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20120423184855.gd30...@an3as.eu -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CADX6M3q4acmJYRSjMzhKA47q5tCkXZh=i4brdipgcdq7vgk...@mail.gmail.com
Re: Injecting abyss into Debian Med Gis repository?
Hi Andreas, Currently ABySS is maintained by me personally, not by Debian-med. Are you proposing adopting the package? Cheers, Shaun On 2012-03-31, at 23:20, Andreas Tille ti...@debian.org wrote: Hi Shaun, when checking the citations of our packages I stumbled upon abyss which is not yet in the Debian Med repository. I would like to do so because the Upstream Metadata Gather is verifying the repositories for changes. As all your packages are currently in Git I guess you will prefer this technique and so I take the freedom to move the current status of abyss into Debian Med Git. I hope you will agree to this. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e36e902b-aef7-4082-9a87-6ba208f09...@gmail.com
Re: Updated Jellyfish
Hi Andreas, I haven't looked at your changes yet, but I trust your judgement. Go ahead and upload. Thanks for your effort. Cheers, Shaun On 2012-03-31, at 0:04, Andreas Tille andr...@an3as.eu wrote: Hi Shaun, you might have noticed that I updated jellyfish in Git. My main motivation was to move the citation information from long description to debian/upstream file as (recently) documented in Debian Med policy. When doing so I upgraded to the latest upstream version. Please tell me if you want to do some other changes or I should upload as is. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/fd193777-f0bc-4971-acf4-de60f16ed...@gmail.com
Accepted abyss 1.3.3-1 (source amd64)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Tue, 13 Mar 2012 15:43:49 -0700 Source: abyss Binary: abyss Architecture: source amd64 Version: 1.3.3-1 Distribution: unstable Urgency: low Maintainer: Shaun Jackman sjack...@debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: abyss - de novo, parallel, sequence assembler for short reads Changes: abyss (1.3.3-1) unstable; urgency=low . * New upstream release. * Some components are dual-licensed BCCA-Academic or GPL-3+. * Bump Standards-Version to 3.9.3. Checksums-Sha1: 4af81d3bdf94503e1abd2dd55ca4f0c404c6bc70 1107 abyss_1.3.3-1.dsc 43985294ba42ee3ed9e8e5eb14d3b1971238a20a 621480 abyss_1.3.3.orig.tar.gz 7bd7ae7c29b6d7d90a62c07aa2a67f975043667a 9003 abyss_1.3.3-1.debian.tar.gz 766b7311bc7a8618a814335731b881e3864dbf31 1709704 abyss_1.3.3-1_amd64.deb Checksums-Sha256: 9882f5850020257e3c90f40b21e9644413d97d062001c95976a09696018d881e 1107 abyss_1.3.3-1.dsc 60396e2c8813952ceb1c66a3ad7c87eda984aa1e4952a14265217d9f639706a0 621480 abyss_1.3.3.orig.tar.gz 570b9fcaf7d641faf7de2ed722520164054bbab57f67be1680f9bd19bcde5a72 9003 abyss_1.3.3-1.debian.tar.gz bf10edab28d514ce9ef5514175c2acd93aee8cf0b76006d4c03967a3a676978e 1709704 abyss_1.3.3-1_amd64.deb Files: 8a57c860d6fcd9e8252f5fb2767b4293 1107 non-free/science optional abyss_1.3.3-1.dsc 15953363d4ef5795d3a82d129e4ca240 621480 non-free/science optional abyss_1.3.3.orig.tar.gz dba856fd1be1e60dce38b8828bc453e6 9003 non-free/science optional abyss_1.3.3-1.debian.tar.gz 013cfafc6a89a9c9f6677deb53a451ec 1709704 non-free/science optional abyss_1.3.3-1_amd64.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAk9f6yoACgkQvFdYF1IwUUrnXgCfRS4hgP5VLlHfxndOJryg2Ghz JLcAn1gRWdfHc2v+Ot2NYl4IrUZpEjtb =ck9z -END PGP SIGNATURE- Accepted: abyss_1.3.3-1.debian.tar.gz to non-free/a/abyss/abyss_1.3.3-1.debian.tar.gz abyss_1.3.3-1.dsc to non-free/a/abyss/abyss_1.3.3-1.dsc abyss_1.3.3-1_amd64.deb to non-free/a/abyss/abyss_1.3.3-1_amd64.deb abyss_1.3.3.orig.tar.gz to non-free/a/abyss/abyss_1.3.3.orig.tar.gz -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1s7cq0-0006tq...@franck.debian.org
Accepted gmap 2011-12-28-1 (source i386)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Thu, 29 Dec 2011 12:32:19 -0800 Source: gmap Binary: gmap Architecture: source i386 Version: 2011-12-28-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: gmap - spliced and SNP-tolerant alignment for mRNA and short reads Changes: gmap (2011-12-28-1) unstable; urgency=low . * New upstream release. Checksums-Sha1: 578fa447e864bb366b9729e9dde4642ef495e1d1 1272 gmap_2011-12-28-1.dsc 9dd75a805668aa2bc3e50cec0f8faf5f69c226fe 3430140 gmap_2011-12-28.orig.tar.gz 12b98b089a651984f624fc1d77860f84d58cae3a 12105 gmap_2011-12-28-1.debian.tar.gz 9cd626fd179da81f0fa02d951379162d34a0699d 6626390 gmap_2011-12-28-1_i386.deb Checksums-Sha256: ebcbe645e04b1ada4b4ceb16c08318a5fff5a71b6a70914cfef79e0a2b272e79 1272 gmap_2011-12-28-1.dsc 0172b6fd00309811df75617937012c73a88c0f8afce4e946fca3d6006cef31d9 3430140 gmap_2011-12-28.orig.tar.gz 3aaccd41b1457fcaa94ed5f0f5c4f1fe32b03d08e86611b1639ffea7c4c3f142 12105 gmap_2011-12-28-1.debian.tar.gz 416435801d11b59219ef3071d5e671786f93b299cd82a970e5c5ccbb12dd6014 6626390 gmap_2011-12-28-1_i386.deb Files: dd2ab2a0170c89e608fb9c3e617cb918 1272 non-free/science optional gmap_2011-12-28-1.dsc cffc0c09f7dd93321b2e1b1ee3da7746 3430140 non-free/science optional gmap_2011-12-28.orig.tar.gz eae8445bd7c87d93cefdabd04070936a 12105 non-free/science optional gmap_2011-12-28-1.debian.tar.gz 5305b935fbd5d3d927ecd1785ab9363a 6626390 non-free/science optional gmap_2011-12-28-1_i386.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAk78074ACgkQvFdYF1IwUUps7ACgtEZB9y1PCy0q/dGloAX9ry4p rVAAnimc9yRIYGN7ewbbM1H0FGc+jRX+ =lmSi -END PGP SIGNATURE- Accepted: gmap_2011-12-28-1.debian.tar.gz to non-free/g/gmap/gmap_2011-12-28-1.debian.tar.gz gmap_2011-12-28-1.dsc to non-free/g/gmap/gmap_2011-12-28-1.dsc gmap_2011-12-28-1_i386.deb to non-free/g/gmap/gmap_2011-12-28-1_i386.deb gmap_2011-12-28.orig.tar.gz to non-free/g/gmap/gmap_2011-12-28.orig.tar.gz -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1rgn82-00031h...@franck.debian.org
[med-svn] [SCM] gmap branch, master, updated. upstream/2011-11-30-31-g1c3f447
The following commit has been merged in the master branch: commit 6d890ec11cda244af878bce40aaf28817d16fa87 Merge: fa026f0479f1ce52255c6f25dba299b7de54d5f6 e4c2005de55d41c725c009e2e1a008c3f46f6b1d Author: Shaun Jackman sjack...@debian.org Date: Thu Dec 29 12:32:02 2011 -0800 Merge commit 'upstream/2011-12-28' -- Align mRNA and EST sequences to a genome ___ 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] [SCM] gmap branch, master, updated. upstream/2011-11-30-31-g1c3f447
The following commit has been merged in the master branch: commit 1c3f4475e101e5ff8f84e51ee2aa9773feddc1db Author: Shaun Jackman sjack...@debian.org Date: Thu Dec 29 12:56:00 2011 -0800 New upstream release. diff --git a/debian/changelog b/debian/changelog index 3809c40..a6732d3 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +gmap (2011-12-28-1) unstable; urgency=low + + * New upstream release. + + -- Shaun Jackman sjack...@debian.org Thu, 29 Dec 2011 12:32:19 -0800 + gmap (2011-11-30-1) unstable; urgency=low * New upstream release. diff --git a/debian/gsnap.1 b/debian/gsnap.1 index ca9500b..1898337 100644 --- a/debian/gsnap.1 +++ b/debian/gsnap.1 @@ -63,6 +63,9 @@ where the 'Y' signifies filtering by chastity. Values: off (default), either, both. For 'either', a 'Y' on either end of a paired-end read will be filtered. For 'both', a 'Y' is required on both ends of a paired-end read (or on the only end of a single-end read). +.TP +\fB--gunzip\fR +Uncompress gzipped input files .SS Computation options .PP -- Align mRNA and EST sequences to a genome ___ 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] [SCM] gmap annotated tag, upstream/2011-12-28, created. upstream/2011-12-28
The annotated tag, upstream/2011-12-28 has been created at a0ccf60d51aa5e17d17c5ec161236dd8558c5b80 (tag) tagging e4c2005de55d41c725c009e2e1a008c3f46f6b1d (commit) replaces upstream/2011-11-30 tagged by Shaun Jackman on Thu Dec 29 12:32:02 2011 -0800 - Shortlog Upstream version 2011-12-28 Shaun Jackman (1): Imported Upstream version 2011-12-28 --- -- Align mRNA and EST sequences to a genome ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
Accepted igv 2.0.30-1 (source all)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Thu, 22 Dec 2011 16:59:30 -0800 Source: igv Binary: igv Architecture: source all Version: 2.0.30-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: igv- Integrative Genomics Viewer Changes: igv (2.0.30-1) unstable; urgency=low . * New upstream release. Checksums-Sha1: ea93d96b13a083271cc33f2aba27ce81c923f10a 1628 igv_2.0.30-1.dsc 840b8d891a50d2885bcfdc8d3146fbf57e510a17 5774595 igv_2.0.30.orig.tar.bz2 1d9032378e0ae205f29a67aff3b25b69d963e4ae 16978 igv_2.0.30-1.debian.tar.gz 01c76ed82bc53a5835b8c7f73d45e7696e06f7a9 7566774 igv_2.0.30-1_all.deb Checksums-Sha256: a6a7dddbe22f3a148b80c9dc491f31140886f75da756309681a0a345cd1874f4 1628 igv_2.0.30-1.dsc 84e4dacbc18f8a65c6085574fdbacee934965e997eb3bf7256ee907dbdf4359f 5774595 igv_2.0.30.orig.tar.bz2 e1eac8c182fe2f81027c47edfd01552f7246db92b285304817286f69ad0e543b 16978 igv_2.0.30-1.debian.tar.gz 5a0f4713575d541611e1baf96776f174a5b44b06c4d0319cb84b8a902423d9d4 7566774 igv_2.0.30-1_all.deb Files: 172507d92e208b754940ab86cb6ae9f6 1628 non-free/science optional igv_2.0.30-1.dsc 748b58c58246119b533ad90faa0e89f9 5774595 non-free/science optional igv_2.0.30.orig.tar.bz2 420383de7abb7b41eb12869daf0cd5c5 16978 non-free/science optional igv_2.0.30-1.debian.tar.gz 395b3abab02c14dc0fa9070756e16d8f 7566774 non-free/science optional igv_2.0.30-1_all.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAk7z1A4ACgkQvFdYF1IwUUroegCfeWhlubtNJd81ZCFuQHsESUi6 zQoAoMs95q/SWs/wHsMrf7zF74Spsa/n =guE/ -END PGP SIGNATURE- Accepted: igv_2.0.30-1.debian.tar.gz to non-free/i/igv/igv_2.0.30-1.debian.tar.gz igv_2.0.30-1.dsc to non-free/i/igv/igv_2.0.30-1.dsc igv_2.0.30-1_all.deb to non-free/i/igv/igv_2.0.30-1_all.deb igv_2.0.30.orig.tar.bz2 to non-free/i/igv/igv_2.0.30.orig.tar.bz2 -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1rdu06-0005v3...@franck.debian.org
Accepted abyss 1.3.2-1 (source i386)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Tue, 13 Dec 2011 17:04:24 -0800 Source: abyss Binary: abyss Architecture: source i386 Version: 1.3.2-1 Distribution: unstable Urgency: low Maintainer: Shaun Jackman sjack...@debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: abyss - de novo, parallel, sequence assembler for short reads Changes: abyss (1.3.2-1) unstable; urgency=low . * New upstream release. Checksums-Sha1: dda337990651116cfbafec8f99b5165fdcc7d504 1107 abyss_1.3.2-1.dsc f13e4ae7ab0724d811628405cd95ea71bc1d9ed1 596973 abyss_1.3.2.orig.tar.gz d1a6cea65d25f08e24066ac2162e9527ebbd3b49 9021 abyss_1.3.2-1.debian.tar.gz 78e351719fbf60da343dd95dddf8645ae04bcf76 1576686 abyss_1.3.2-1_i386.deb Checksums-Sha256: f7f7b3d48524663f02528a6ea1e8cdde8ffdcdacd37cf66e70f0e5e72ff5a5c2 1107 abyss_1.3.2-1.dsc 0086931784dd41244e335f622a337df328faf1c8138f87dd6f7d245bb3b0c049 596973 abyss_1.3.2.orig.tar.gz 1f7aeb9800cb54721f9688e33823d473d9301ffb77088874b7df3ac89c6760f6 9021 abyss_1.3.2-1.debian.tar.gz fd4db333485d8362b2bab881ed9ee12147eedf119b8eb1fa08f38a91bcf007b4 1576686 abyss_1.3.2-1_i386.deb Files: 295d2758062aaa57183af36550a5e35a 1107 non-free/science optional abyss_1.3.2-1.dsc a7551c95f33a0c61cab50bc35db347e4 596973 non-free/science optional abyss_1.3.2.orig.tar.gz e83a26de7a5cc53db9ab403aa4bea060 9021 non-free/science optional abyss_1.3.2-1.debian.tar.gz 7aed7c28969dca29a3df9d7d5f2362a1 1576686 non-free/science optional abyss_1.3.2-1_i386.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAk7oB8QACgkQvFdYF1IwUUrVMgCgvpIb0Bew2cpRDqs8xHcwFw7F lkwAnjl/COo7PXst8aSH+k/P/ODQ/1Tc =RJ8L -END PGP SIGNATURE- Accepted: abyss_1.3.2-1.debian.tar.gz to non-free/a/abyss/abyss_1.3.2-1.debian.tar.gz abyss_1.3.2-1.dsc to non-free/a/abyss/abyss_1.3.2-1.dsc abyss_1.3.2-1_i386.deb to non-free/a/abyss/abyss_1.3.2-1_i386.deb abyss_1.3.2.orig.tar.gz to non-free/a/abyss/abyss_1.3.2.orig.tar.gz -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1raesc-0004ws...@franck.debian.org
Accepted gmap 2011-11-30-1 (source i386)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Wed, 07 Dec 2011 10:46:12 -0800 Source: gmap Binary: gmap Architecture: source i386 Version: 2011-11-30-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: gmap - spliced and SNP-tolerant alignment for mRNA and short reads Changes: gmap (2011-11-30-1) unstable; urgency=low . * New upstream release. Checksums-Sha1: 11304ac3bee1dd5485d5c9b589fe8c0d27cff2aa 1272 gmap_2011-11-30-1.dsc c024d1a6bf3f9f0106955e087dc56d698351e694 3429798 gmap_2011-11-30.orig.tar.gz 336b98995695a2eb43bbcf1d64e2d5965d840cd6 12149 gmap_2011-11-30-1.debian.tar.gz defeffebc253eaa159d80ba9e556cedfa724b1fb 6623896 gmap_2011-11-30-1_i386.deb Checksums-Sha256: 1f4f546e784f1ed536647db4b2b5b0a2bd1431eafed977216b55adc0e347f6ed 1272 gmap_2011-11-30-1.dsc 1dda24eeb2403b5ad834c9a3f34c440170187ed77e11336562fe45b29d9545db 3429798 gmap_2011-11-30.orig.tar.gz efbfb36f620d3f74cb89f76b9fa83ca8ac639e9eba240f6f1eb6e19776909365 12149 gmap_2011-11-30-1.debian.tar.gz 9f4e251d3419fe49285e5274bc0f10f13702bd2f4a2f65d4cbb48d0ff136139e 6623896 gmap_2011-11-30-1_i386.deb Files: 5956be38b23e270f4d641cb72e96dbe8 1272 non-free/science optional gmap_2011-11-30-1.dsc 92936e83d218b9aab42870c44996ff35 3429798 non-free/science optional gmap_2011-11-30.orig.tar.gz f2139ba04ba925f90918fd5ae527657d 12149 non-free/science optional gmap_2011-11-30-1.debian.tar.gz dbd5101575f684451e965a872cbf3e2e 6623896 non-free/science optional gmap_2011-11-30-1_i386.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAk7f2HwACgkQvFdYF1IwUUqoOwCgzT0pldf5FidCQDEUi+XlDztI TPAAn23Owh6+RotIOIFhJLUDYJfh6IES =b2Bx -END PGP SIGNATURE- Accepted: gmap_2011-11-30-1.debian.tar.gz to non-free/g/gmap/gmap_2011-11-30-1.debian.tar.gz gmap_2011-11-30-1.dsc to non-free/g/gmap/gmap_2011-11-30-1.dsc gmap_2011-11-30-1_i386.deb to non-free/g/gmap/gmap_2011-11-30-1_i386.deb gmap_2011-11-30.orig.tar.gz to non-free/g/gmap/gmap_2011-11-30.orig.tar.gz -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1ryp7b-o4...@franck.debian.org
[med-svn] [SCM] gmap branch, master, updated. upstream/2011-10-16-29-gfa026f0
The following commit has been merged in the master branch: commit fa026f0479f1ce52255c6f25dba299b7de54d5f6 Author: Shaun Jackman sjack...@debian.org Date: Wed Dec 7 13:21:47 2011 -0800 New upstream release. diff --git a/debian/changelog b/debian/changelog index 758ddfb..3809c40 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +gmap (2011-11-30-1) unstable; urgency=low + + * New upstream release. + + -- Shaun Jackman sjack...@debian.org Wed, 07 Dec 2011 10:46:12 -0800 + gmap (2011-10-16-1) unstable; urgency=low * New upstream release. diff --git a/debian/gmap.1 b/debian/gmap.1 index 6958409..37a581a 100644 --- a/debian/gmap.1 +++ b/debian/gmap.1 @@ -1,4 +1,4 @@ -.TH GMAP 1 August 2011 GMAP 2011-08-15 User Commands +.TH GMAP 1 Nov 2011 GMAP 2011-11-30 User Commands .SH NAME gmap \- Genomic Mapping and Alignment Program .SH SYNOPSIS @@ -84,7 +84,8 @@ Max total intron length (default 240) Amount of unaligned sequence that triggers search for the remaining sequence (default 40). Enables alignment of chimeric reads, and may help -with some non-chimeric reads. To turn off, set to 0. +with some non-chimeric reads. To turn off, set to +a large value (greater than the query length). .TP \fB\-t\fR, \fB\-\-nthreads\fR=\fIINT\fR Number of worker threads @@ -175,6 +176,11 @@ prints two paths if chimera detected, else one. If more than maximum number of paths are found, then nothing is printed. .TP +\fB--suboptimal-score\fR=\fIINT\fR +Report only paths whose score is within this value of the +best path. By default, if this option is not provided, +the program prints all paths found. +.TP \fB\-O\fR, \fB\-\-ordered\fR Print output in same order as input (relevant only if there is more than one worker thread) @@ -226,10 +232,6 @@ Options for SAM output \fB\-\-no\-sam\-headers\fR Do not print headers beginning with '@' .TP -\fB\-\-noncanonical\-splices\fR=\fISTRING\fR -Print non-canonical genomic gaps greater than 20 nt -in CIGAR string as STRING. Allowed values: N (default), D. -.TP \fB\-\-read\-group\-id\fR=\fISTRING\fR Value to put into read-group id (RG-ID) field .TP diff --git a/debian/gmap_setup.1 b/debian/gmap_setup.1 index 8338d17..aab9a93 100644 --- a/debian/gmap_setup.1 +++ b/debian/gmap_setup.1 @@ -1,4 +1,4 @@ -.TH GMAP_SETUP 1 Aug 2010 GMAP 2010-07-27 User Commands +.TH GMAP_SETUP 1 Nov 2011 GMAP 2011-11-30 User Commands .SH NAME gmap_setup \- create a genome database for GMAP or GSNAP .SH SYNOPSIS diff --git a/debian/gsnap.1 b/debian/gsnap.1 index a70434b..ca9500b 100644 --- a/debian/gsnap.1 +++ b/debian/gsnap.1 @@ -1,4 +1,4 @@ -.TH GSNAP 1 August 2011 GMAP 2011-08-15 User Commands +.TH GSNAP 1 Nov 2011 GMAP 2011-11-30 User Commands .SH NAME gsnap \- Genomic Short-read Nucleotide Alignment Program .SH SYNOPSIS @@ -104,8 +104,14 @@ Whether to count unknown (N) characters in the genome as a mismatch .TP \fB--terminal-threshold\fR=\fIINT\fR Threshold for searching for a terminal alignment (from one end of the -read to the best possible position at the other end) (default 3). -To turn off terminal alignments, set this to a high value. +read to the best possible position at the other end) (default 2). +For example, if this value is 2, then if GSNAP finds an exact or +1-mismatch alignment, it will not try to find a terminal alignment. +Note that this default value may not be low enough if you want to +obtain terminal alignments for very short reads, although such reads +probably don't have enough specificity for terminal alignments anyway. +To turn off terminal alignments, set this to a high value, greater +than the value for --max-mismatches. .TP \fB\-i\fR, \fB\-\-indel\-penalty\fR=\fIINT\fR Penalty for an indel (default 2). @@ -141,7 +147,13 @@ To turn off, use the value off. .TP \fB\-\-trim\-mismatch\-score\fR=\fIINT\fR Score to use for mismatches when trimming at ends (default is -3; -to turn off trimming, specify 0) +to turn off trimming, specify 0). Warning: turning trimming off +will give false positive mismatches at the ends of reads +.TP +\fB--trim-indel-score\fR=\fIINT\fR +Score to use for indels when trimming at ends (default is -4; +to turn off trimming, specify 0). Warning: turning trimming off +will give false positive indels at the ends of reads .TP \fB\-V\fR, \fB\-\-snpsdir\fR=\fISTRING\fR Directory for SNPs index files (created using snpindex) (default is @@ -230,6 +242,12 @@ Look for splicing involving known sites or known introns See README instructions for the distinction between known sites and known introns .TP +\fB--ambig-splice-noclip\fR +For ambiguous known splicing at ends of the read, do not clip at the +splice site, but extend instead into the intron. This flag makes +sense only if you provide the --use-splicing flag, and you are trying +to eliminate all soft clipping with --trim-mismatch-score=0 +.TP \fB\-w\fR, \fB\-\-localsplicedist\fR=\fIINT\fR Definition of local novel splicing event (default 20
[med-svn] [SCM] gmap branch, pristine-tar, updated. 0a460b1ec9046adeea6f79f02b1dc3c800249dde
The following commit has been merged in the pristine-tar branch: commit 0a460b1ec9046adeea6f79f02b1dc3c800249dde Author: Shaun Jackman sjack...@debian.org Date: Wed Dec 7 10:46:06 2011 -0800 pristine-tar data for gmap_2011-11-30.orig.tar.gz diff --git a/gmap_2011-11-30.orig.tar.gz.delta b/gmap_2011-11-30.orig.tar.gz.delta new file mode 100644 index 000..9d2c6bd Binary files /dev/null and b/gmap_2011-11-30.orig.tar.gz.delta differ diff --git a/gmap_2011-11-30.orig.tar.gz.id b/gmap_2011-11-30.orig.tar.gz.id new file mode 100644 index 000..a123783 --- /dev/null +++ b/gmap_2011-11-30.orig.tar.gz.id @@ -0,0 +1 @@ +97f37c8aff7a03672cc366c437fd58ce1dd064de -- Align mRNA and EST sequences to a genome ___ 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] [SCM] gmap branch, master, updated. upstream/2011-10-16-29-gfa026f0
The following commit has been merged in the master branch: commit 3efcc56440643d5fdf174b9c05f0e19f7b9d3484 Merge: f9ff31c8c859f6aeee6045ae86eda7bf4b98b865 97f37c8aff7a03672cc366c437fd58ce1dd064de Author: Shaun Jackman sjack...@debian.org Date: Wed Dec 7 10:46:06 2011 -0800 Merge commit 'upstream/2011-11-30' -- Align mRNA and EST sequences to a genome ___ 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] [SCM] gmap annotated tag, upstream/2011-11-30, created. upstream/2011-11-30
The annotated tag, upstream/2011-11-30 has been created at 94e7a81eb25188390d5180666c792d07044674e2 (tag) tagging 97f37c8aff7a03672cc366c437fd58ce1dd064de (commit) replaces upstream/2011-10-16 tagged by Shaun Jackman on Wed Dec 7 10:46:06 2011 -0800 - Shortlog Upstream version 2011-11-30 Shaun Jackman (1): Imported Upstream version 2011-11-30 --- -- Align mRNA and EST sequences to a genome ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
Accepted avarice 2.11-1 (source i386)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Sat, 03 Dec 2011 12:23:50 -0800 Source: avarice Binary: avarice Architecture: source i386 Version: 2.11-1 Distribution: unstable Urgency: low Maintainer: Shaun Jackman sjack...@debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: avarice- use GDB with Atmel's JTAG ICE for the AVR Closes: 603630 Changes: avarice (2.11-1) unstable; urgency=low . * New upstream release. * Replace SYSFS with ATTRS in avarice.rules. Closes: #603630. Thanks to Gonzalo Pérez de Olaguer Córdoba. * Update the Debian policy to version 3.9.2. * Bump debhelper to version 8. Checksums-Sha1: d2663663a4c030e0545b72da05c8534e00caf06e 1011 avarice_2.11-1.dsc c482e897ce03c2e98615163c58942139374e3738 217314 avarice_2.11.orig.tar.gz 34287a19abf5ce88f25164069f2bcfbfbdfbdf17 2530 avarice_2.11-1.diff.gz b9d4ba11fd8cfa1f5e0822f0abf68ed01e5af833 424358 avarice_2.11-1_i386.deb Checksums-Sha256: ef4155aa344ab43b9ad02e456171c2d327fd03f4ad7b828e5858c6b939c37269 1011 avarice_2.11-1.dsc 22fd36b508dc901cf9540e644fbf332b0e07c6d4117093c3f9d8b6f67634bc92 217314 avarice_2.11.orig.tar.gz e1a035ef40062365b095e25f0513d87afb3b726484314f25293d3430b3b981c0 2530 avarice_2.11-1.diff.gz 3a554e9e35fa1f130c8f450486dd79eedb377106148aea651290e99dbbec4a65 424358 avarice_2.11-1_i386.deb Files: a7afaf7d6e12a1447d05a77b02cdc6d8 1011 electronics optional avarice_2.11-1.dsc a1d17150a22a07374ae371579ad857ab 217314 electronics optional avarice_2.11.orig.tar.gz 2de1713194c385ae5db65d2f18179c8d 2530 electronics optional avarice_2.11-1.diff.gz 2be37ac8a1f8382307999cad63e6b907 424358 electronics optional avarice_2.11-1_i386.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAk7ajpUACgkQvFdYF1IwUUr48ACfUUSBiXTCddxfOYmNObqM0sdq Ph0AnjZm00/PSAkfc+VV6IPRywNimfYD =RRtC -END PGP SIGNATURE- Accepted: avarice_2.11-1.diff.gz to main/a/avarice/avarice_2.11-1.diff.gz avarice_2.11-1.dsc to main/a/avarice/avarice_2.11-1.dsc avarice_2.11-1_i386.deb to main/a/avarice/avarice_2.11-1_i386.deb avarice_2.11.orig.tar.gz to main/a/avarice/avarice_2.11.orig.tar.gz -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1rwxqn-0008va...@franck.debian.org
Accepted pptview 8.0-7 (source i386)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Sat, 03 Dec 2011 12:48:15 -0800 Source: pptview Binary: pptview Architecture: source i386 Version: 8.0-7 Distribution: unstable Urgency: low Maintainer: Shaun Jackman sjack...@debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: pptview- view PowerPoint presentations Closes: 598216 Changes: pptview (8.0-7) unstable; urgency=low . * Add amd64 to Architecture. Closes: #598216. * Update Debian policy to version 3.9.2. * Bump debhelper compat to version 8. Checksums-Sha1: b38c024afac2ae3b339733c5ac00e58b248afe4b 940 pptview_8.0-7.dsc 47d3a93dae4214bbe4bdf56b970ec0bc867736ad 7336 pptview_8.0-7.diff.gz f720d2cb0d3787668e603122cc5fa131b96196cb 1794678 pptview_8.0-7_i386.deb Checksums-Sha256: a7aaf5771a3c0363c1442c87ee35ecd10d6b3a926d3f369973bbdef71fd9c980 940 pptview_8.0-7.dsc aaa9cf35691f3d368b6f81af63894e1184aa38cfe6208124bbf2aca863384142 7336 pptview_8.0-7.diff.gz dd43ec8a646ec59d2d82d03879a1c2c90c503abdd89477b675d94eb5dcc57e84 1794678 pptview_8.0-7_i386.deb Files: 531b0c9b5ba547294390153217e8bfe4 940 non-free/text optional pptview_8.0-7.dsc bbbc46fdcfc3864324d4d3dca87c127e 7336 non-free/text optional pptview_8.0-7.diff.gz fe56a478caddc51bfe4ea23fe2d58be2 1794678 non-free/text optional pptview_8.0-7_i386.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAk7ajWMACgkQvFdYF1IwUUp7kwCgu9lyMcTtVYzYW4taWWTKFimk oUAAoMPsqIUl9s1DhvU5EAauMayARcbi =mmUh -END PGP SIGNATURE- Accepted: pptview_8.0-7.diff.gz to non-free/p/pptview/pptview_8.0-7.diff.gz pptview_8.0-7.dsc to non-free/p/pptview/pptview_8.0-7.dsc pptview_8.0-7_i386.deb to non-free/p/pptview/pptview_8.0-7_i386.deb -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1rwxa0-0002ir...@franck.debian.org
Bug#605421: pptview: Please make sure to reduce the dependencies
pptview is a PE32 executable, so wine is necessary. Cheers, Shaun On 29 November 2010 12:13, Frenchn00b frenchn...@yahoo.com wrote: Package: pptview Severity: important Non non-substancial needed dependencies are in the deb file. wine dependencies, could you avoid that too please ? a# apt-get install abiword pptview Reading package lists... Done Building dependency tree Reading state information... Done abiword is already the newest version. The following extra packages will be installed: cups-bsd libwine libwine-alsa libwine-cms libwine-gl libwine-gphoto2 libwine-ldap libwine-print libwine-sane wine wine-bin wine-utils Suggested packages: wine-doc openoffice.org-impress binfmt-support ttf-mscorefonts-installer avscan klamav clamav The following NEW packages will be installed: cups-bsd libwine libwine-alsa libwine-cms libwine-gl libwine-gphoto2 libwine-ldap libwine-print libwine-sane pptview wine wine-bin wine-utils 0 upgraded, 13 newly installed, 0 to remove and 59 not upgraded. Need to get 12.9MB of archives. After this operation, 57.0MB of additional disk space will be used. Do you want to continue [Y/n]? y best regards -- System Information: Debian Release: squeeze/sid APT prefers testing APT policy: (500, 'testing') Architecture: i386 (i686) Kernel: Linux 2.6.32-5-686 (SMP w/2 CPU cores) Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Accepted abyss 1.3.1-1 (source amd64)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Mon, 24 Oct 2011 11:32:59 -0700 Source: abyss Binary: abyss Architecture: source amd64 Version: 1.3.1-1 Distribution: unstable Urgency: low Maintainer: Shaun Jackman sjack...@debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: abyss - de novo, parallel, sequence assembler for short reads Changes: abyss (1.3.1-1) unstable; urgency=low . * New upstream release. Checksums-Sha1: 332e1cc184ab4689a0c7e18a75212b287b8db00e 1107 abyss_1.3.1-1.dsc 713d928552660e7b9a95f75911451a134a94b5bd 597660 abyss_1.3.1.orig.tar.gz 11d7a2d11dee7ac8ceeb6f191a2d23842b66b2c0 8794 abyss_1.3.1-1.debian.tar.gz 7bddd63f6fce2a8f1fa8d238c3ed8693fa01b805 1360726 abyss_1.3.1-1_amd64.deb Checksums-Sha256: 03004172947a0ecd58e61c8f6eaa4f73af0e0ec3f1850c9132020a42b2710356 1107 abyss_1.3.1-1.dsc e7dcca68f6607c384ad6a69419741eaf0a99a6de41bdea200ee64a129a529171 597660 abyss_1.3.1.orig.tar.gz b83156e86c13f8a035ee22581c07048cce1ec3926d2caa7b6716877e21bd4124 8794 abyss_1.3.1-1.debian.tar.gz 0ecffabff9d53072e1d9ffbe2127f7834edb84d7e040fb550250a8f2181054e2 1360726 abyss_1.3.1-1_amd64.deb Files: c72728894dd414df4f80c49dae92540c 1107 non-free/science optional abyss_1.3.1-1.dsc ba9f8e65a8356195a12a623c9b3b97a9 597660 non-free/science optional abyss_1.3.1.orig.tar.gz 71da3f032609d4c1d5cd3c9bdb0097e8 8794 non-free/science optional abyss_1.3.1-1.debian.tar.gz 23e1d889fd5ed73915dfd812ff79152d 1360726 non-free/science optional abyss_1.3.1-1_amd64.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) iEYEARECAAYFAk6lwlEACgkQvFdYF1IwUUr1UACgm+Wl7T7kDVs/RVrqe9BQWIIo VL0AoKdMXITQKyqsZBVRmsvUFdQ1cXFt =vioq -END PGP SIGNATURE- Accepted: abyss_1.3.1-1.debian.tar.gz to non-free/a/abyss/abyss_1.3.1-1.debian.tar.gz abyss_1.3.1-1.dsc to non-free/a/abyss/abyss_1.3.1-1.dsc abyss_1.3.1-1_amd64.deb to non-free/a/abyss/abyss_1.3.1-1_amd64.deb abyss_1.3.1.orig.tar.gz to non-free/a/abyss/abyss_1.3.1.orig.tar.gz -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1rirex-0008w3...@franck.debian.org
Accepted gmap 2011-10-16-1 (source i386)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Wed, 19 Oct 2011 15:40:36 -0700 Source: gmap Binary: gmap Architecture: source i386 Version: 2011-10-16-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: gmap - spliced and SNP-tolerant alignment for mRNA and short reads Changes: gmap (2011-10-16-1) unstable; urgency=low . * New upstream release. Checksums-Sha1: a2cbfa392714cad475ebf0f6c6167c9ece9adb12 1272 gmap_2011-10-16-1.dsc 22be240ab4d7ac3284acfeba730bd548bde423d5 3407282 gmap_2011-10-16.orig.tar.gz 4b1644d1603c14d6aea64cbd9c8ef71fde2ea8b8 11391 gmap_2011-10-16-1.debian.tar.gz 321025754dfc01edd8a4fe580770dd46dc40189e 6602920 gmap_2011-10-16-1_i386.deb Checksums-Sha256: 2cb10f96167de32d30d66cbb4197c343f861a6278fb3da49444055979276a0c5 1272 gmap_2011-10-16-1.dsc 5b7c0ec361ce2e8657c2db8c36a81e220e72f0441a1bf7243ad83c8d561792d9 3407282 gmap_2011-10-16.orig.tar.gz 215cd60d485c8a70d18eaaae76acd9b07b343df1a07a7ffa97d756c38b6dbb24 11391 gmap_2011-10-16-1.debian.tar.gz 61ec7095c3f39d29a650cd22d456991055e42078b3302c17d89b9ea67c3ef882 6602920 gmap_2011-10-16-1_i386.deb Files: 076d1af600875e54445a7ccbc2fb4ffd 1272 non-free/science optional gmap_2011-10-16-1.dsc 4ddba296346def777cb68bff921c38fc 3407282 non-free/science optional gmap_2011-10-16.orig.tar.gz dcb9f8639a584af3a1a6611eae2e066c 11391 non-free/science optional gmap_2011-10-16-1.debian.tar.gz 02b0c2e224f14b2eaae051aac7a716cd 6602920 non-free/science optional gmap_2011-10-16-1_i386.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAk6fYqQACgkQvFdYF1IwUUppGACgouexpuf02LjvVYAiGzRj3ZOG STAAnidVCLhs0/jkpbKoaOftMpevgh+I =OKMZ -END PGP SIGNATURE- Accepted: gmap_2011-10-16-1.debian.tar.gz to non-free/g/gmap/gmap_2011-10-16-1.debian.tar.gz gmap_2011-10-16-1.dsc to non-free/g/gmap/gmap_2011-10-16-1.dsc gmap_2011-10-16-1_i386.deb to non-free/g/gmap/gmap_2011-10-16-1_i386.deb gmap_2011-10-16.orig.tar.gz to non-free/g/gmap/gmap_2011-10-16.orig.tar.gz -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1rggjs-0002no...@franck.debian.org
[med-svn] [SCM] gmap branch, master, updated. upstream/2011-09-14-27-gf9ff31c
The following commit has been merged in the master branch: commit a0a5398d71ef463913157876817c016e727bf6a5 Merge: 2d7fb22fd04e815078965cd2e7827bc7ae82cc67 9901f2c730069572df57ef5bbc05538a459c508d Author: Shaun Jackman sjack...@debian.org Date: Wed Oct 19 15:40:32 2011 -0700 Merge commit 'upstream/2011-10-16' -- Align mRNA and EST sequences to a genome ___ 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] [SCM] gmap branch, master, updated. upstream/2011-09-14-27-gf9ff31c
The following commit has been merged in the master branch: commit f9ff31c8c859f6aeee6045ae86eda7bf4b98b865 Author: Shaun Jackman sjack...@debian.org Date: Wed Oct 19 16:57:17 2011 -0700 New upstream release. diff --git a/debian/changelog b/debian/changelog index c348c40..758ddfb 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +gmap (2011-10-16-1) unstable; urgency=low + + * New upstream release. + + -- Shaun Jackman sjack...@debian.org Wed, 19 Oct 2011 15:40:36 -0700 + gmap (2011-09-14-1) unstable; urgency=low * New upstream release. diff --git a/debian/gmap.1 b/debian/gmap.1 index dc1d6a8..6958409 100644 --- a/debian/gmap.1 +++ b/debian/gmap.1 @@ -67,6 +67,10 @@ If mmap not available and allocate not chosen, then will use fileio Turns off splicing (useful for aligning genomic sequences onto a genome) .TP +\fB--min-intronlength\fR=\fIINT\fR +Min length for one internal intron (default 9). Below this size, +a genomic gap will be considered a deletion rather than an intron. +.TP \fB-K\fR, \fB--intronlength\fR=\fIINT\fR Max length for one internal intron (default 100) .TP diff --git a/debian/gsnap.1 b/debian/gsnap.1 index 0578686..a70434b 100644 --- a/debian/gsnap.1 +++ b/debian/gsnap.1 @@ -36,7 +36,7 @@ Amount of barcode to remove from start of read (default 0) \fB\-o\fR, \fB\-\-orientation=\fISTRING\fR Orientation of paired-end reads Allowed values: FR (fwd-rev, or typical Illumina; default), -FR (rev-fwd, for circularized inserts), or FF (fwd-fwd, same strand) +RF (rev-fwd, for circularized inserts), or FF (fwd-fwd, same strand) .TP \fB--fastq-id-start\fR=\fIINT\fR Starting position of identifier in FASTQ header, space-delimited (= 1) @@ -44,7 +44,9 @@ Starting position of identifier in FASTQ header, space-delimited (= 1) \fB--fastq-id-end\fR=\fIINT\fR Ending position of identifier in FASTQ header, space-delimited (= 1) Examples: - @HWUSI-EAS100R:6:73:941:1973#0/1 start=1, end=1 (default) + @HWUSI-EAS100R:6:73:941:1973#0/1 + start=1, end=1 (default) + = identifier is HWUSI-EAS100R:6:73:941:1973#0 @SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36 start=1, end=1 = identifier is SRR001666.1 @@ -52,6 +54,15 @@ Ending position of identifier in FASTQ header, space-delimited (= 1) = identifier is 071112_SLXA-EAS1_s_7:5:1:817:345 start=1, end=2 = identifier is SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 +.TP +\fB--filter-chastity\fR=\fISTRING\fR +Skips reads marked by the Illumina chastity program. Expecting a string +after the accession having a 'Y' after the first colon, like this: + @accession 1:Y:0:CTTGTA +where the 'Y' signifies filtering by chastity. +Values: off (default), either, both. For 'either', a 'Y' on either end +of a paired-end read will be filtered. For 'both', a 'Y' is required +on both ends of a paired-end read (or on the only end of a single-end read). .SS Computation options .PP @@ -150,7 +161,9 @@ Directory for A-to-I RNA editing index files (created using atoiindex) -d) .TP \fB--mode\fR=\fISTRING\fR -Alignment mode: standard (default), cmet, or atoi +Alignment mode: standard (default), cmet-stranded, cmet-nonstranded, +atoi-stranded, or atoi-nonstranded. Non-standard modes requires you +to have previously run the cmetindex or atoiindex programs on the genome .TP \fB--tallydir\fR=\fISTRING\fR Directory for tally IIT file to resolve concordant multiple results @@ -199,62 +212,44 @@ Perform GMAP improvement on nearby genomic regions up to this many Allow microexons only if one of the splice site probabilities is greater than this value (default 0.90) .SS -Genes options for RNA-Seq -.TP -\fB-g, --genes\fR=\fISTRING\fR -Look for known genes in STRING.iit, to be used for resolving -multiple mapping reads. See README instructions for the correct -formatting of a genes IIT file. -.TP -\fB--favor-multiexon\fR -In resolving multiple mapping reads, overlaps with known -multi-exon genes are favored over those with known single-exon -genes. This favors spliced genes over psuedogenes. -.SS Splicing options for RNA\-Seq .TP .TP \fB-N,\fR \fB--novelsplicing\fR=\fIINT\fR Look for novel splicing (0=no (default), 1=yes) .TP -\fB-S\fR, \fB--splicesdir\fR=\fISTRING\fR +\fB--splicingdir\fR=\fISTRING\fR Directory for splicing involving known sites or known introns, -as specified by the -s or --use-splices flag (default is +as specified by the -s or --use-splicing flag (default is directory computed from -D and -d flags). Note: can just give full pathname to the -s flag instead. .TP -\fB\-s\fR, \fB--use-splices\fR=\fISTRING\fR +\fB\-s\fR, \fB--use-splicing\fR=\fISTRING\fR Look for splicing involving known sites or known introns (in STRING.iit), at short or long distances. See README instructions for the distinction between known sites and known introns .TP -\fB\-\-novel\-doublesplices\fR -Allow GSNAP to look for two splices in a single-end involving novel -splice sites (default is not to allow
[med-svn] [SCM] gmap branch, pristine-tar, updated. 3273d61e4cf5005e041b9b3913a5767ef9936caf
The following commit has been merged in the pristine-tar branch: commit 3273d61e4cf5005e041b9b3913a5767ef9936caf Author: Shaun Jackman sjack...@debian.org Date: Wed Oct 19 15:40:32 2011 -0700 pristine-tar data for gmap_2011-10-16.orig.tar.gz diff --git a/gmap_2011-10-16.orig.tar.gz.delta b/gmap_2011-10-16.orig.tar.gz.delta new file mode 100644 index 000..77d1b8c Binary files /dev/null and b/gmap_2011-10-16.orig.tar.gz.delta differ diff --git a/gmap_2011-10-16.orig.tar.gz.id b/gmap_2011-10-16.orig.tar.gz.id new file mode 100644 index 000..2aa9f00 --- /dev/null +++ b/gmap_2011-10-16.orig.tar.gz.id @@ -0,0 +1 @@ +9901f2c730069572df57ef5bbc05538a459c508d -- Align mRNA and EST sequences to a genome ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
Accepted jellyfish 1.1.2-1 (source amd64)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Mon, 10 Oct 2011 11:49:11 -0700 Source: jellyfish Binary: jellyfish Architecture: source amd64 Version: 1.1.2-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: jellyfish - count k-mers in DNA sequences Closes: 644925 Changes: jellyfish (1.1.2-1) unstable; urgency=low . * Initial release. Closes: #644925. Checksums-Sha1: 7d2b5587036d6a6a93252e912c5dab7fa0b58515 1281 jellyfish_1.1.2-1.dsc 3e1abdd6140bd48ec1aee7432a3e71046a2cb53c 847656 jellyfish_1.1.2.orig.tar.gz 9878e9874c37b09edf6b0582fe1a56c57c32197c 3444 jellyfish_1.1.2-1.debian.tar.gz f022b6d2a3e66ec15bd61331c47ef46ccb6d9ed6 378664 jellyfish_1.1.2-1_amd64.deb Checksums-Sha256: a73f930230136abda89ff63f83085483704f70442e74ebf8d9d148d04409726c 1281 jellyfish_1.1.2-1.dsc 746ef64a3c1ec5f458398b1a6239ad683f4c02b86ca63436180cac38316ed98d 847656 jellyfish_1.1.2.orig.tar.gz 783d0a72a486dbd7273db4311facf8892eeb0cc4f778fa3530c25a7c0e1d5b3c 3444 jellyfish_1.1.2-1.debian.tar.gz d212e2af021b80bf5a06cde0281443cd19c7cfb1af2da6cfbcf580c1bba761ff 378664 jellyfish_1.1.2-1_amd64.deb Files: a06f54636cc1315573acd1787bca4330 1281 science optional jellyfish_1.1.2-1.dsc c2c167d8ac347f163a7d77c75537e97e 847656 science optional jellyfish_1.1.2.orig.tar.gz 55217413e0e617193dd86c7285014b36 3444 science optional jellyfish_1.1.2-1.debian.tar.gz b07c136d859e223f69450566450aa9c8 378664 science optional jellyfish_1.1.2-1_amd64.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) iEYEARECAAYFAk6TYXMACgkQvFdYF1IwUUoNTQCaAjZqWh1MdXCf65yrfczOAHat /Y4An3C3/RFT8SjH+TEmcsOtGY6esgJm =x8X3 -END PGP SIGNATURE- Accepted: jellyfish_1.1.2-1.debian.tar.gz to main/j/jellyfish/jellyfish_1.1.2-1.debian.tar.gz jellyfish_1.1.2-1.dsc to main/j/jellyfish/jellyfish_1.1.2-1.dsc jellyfish_1.1.2-1_amd64.deb to main/j/jellyfish/jellyfish_1.1.2-1_amd64.deb jellyfish_1.1.2.orig.tar.gz to main/j/jellyfish/jellyfish_1.1.2.orig.tar.gz -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1rdfjs-0004rh...@franck.debian.org
Bug#644925: ITP: jellyfish -- count k-mers of DNA
Package: wnpp Severity: wishlist Package name: jellyfish Version: 1.1.2 Upstream author: Guillaume Marçais gmarc...@umd.edu License: GPL-3+ Description: count k-mers of DNA JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the compare-and-swap CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the jellyfish dump command. . If you use JELLYFISH in your research, please cite: Guillaume Marcais and Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics (2011) 27(6): 764-770 (first published online January 7, 2011) doi:10.1093/bioinformatics/btr011 -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#644925: ITP: jellyfish -- count k-mers of DNA
Package: wnpp Severity: wishlist Package name: jellyfish Version: 1.1.2 Upstream author: Guillaume Marçais gmarc...@umd.edu License: GPL-3+ Description: count k-mers of DNA JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the compare-and-swap CPU instruction to increase parallelism. . JELLYFISH is a command-line program that reads FASTA and multi-FASTA files containing DNA sequences. It outputs its k-mer counts in an binary format, which can be translated into a human-readable text format using the jellyfish dump command. . If you use JELLYFISH in your research, please cite: Guillaume Marcais and Carl Kingsford, A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics (2011) 27(6): 764-770 (first published online January 7, 2011) doi:10.1093/bioinformatics/btr011 -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/cadx6m3qbqzerguuzg_ysdxpowd13g6uzev6vxagaax7jbkv...@mail.gmail.com
[med-svn] [SCM] jellyfish branch, master, created. 50f2f49253b432acdb224e4cc94ce856c4d6991a
The branch, master has been created at 50f2f49253b432acdb224e4cc94ce856c4d6991a (commit) - Shortlog commit 50f2f49253b432acdb224e4cc94ce856c4d6991a Author: Shaun Jackman sjack...@gmail.com Date: Mon Oct 10 11:33:20 2011 -0700 Imported Upstream version 1.1.2 --- -- count k-mers of DNA ___ 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] [SCM] jellyfish branch, master, updated. 6529ac1a2916faf781c227cd16dfab240bc57611
The following commit has been merged in the master branch:
commit 6529ac1a2916faf781c227cd16dfab240bc57611
Author: Shaun Jackman sjack...@gmail.com
Date: Mon Oct 10 14:04:37 2011 -0700
Initial release.
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 000..0c2418b
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+jellyfish (1.1.2-1) unstable; urgency=low
+
+ * Initial release. Closes: #644925.
+
+ -- Shaun Jackman sjack...@debian.org Mon, 10 Oct 2011 11:49:11 -0700
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 000..7f8f011
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+7
diff --git a/debian/control b/debian/control
new file mode 100644
index 000..99b4c01
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,36 @@
+Source: jellyfish
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team
debian-med-packag...@lists.alioth.debian.org
+DM-Upload-Allowed: yes
+Uploaders: Shaun Jackman sjack...@debian.org
+Build-Depends: debhelper (= 7.0.50~)
+Standards-Version: 3.9.2
+Homepage: http://www.cbcb.umd.edu/software/jellyfish/
+Vcs-Git: git://git.debian.org/git/debian-med/jellyfish.git
+Vcs-Browser: http://git.debian.org/?p=debian-med/jellyfish.git
+
+
+Package: jellyfish
+Architecture: any-amd64
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: count k-mers in DNA sequences
+ JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
+ DNA. A k-mer is a substring of length k, and counting the occurrences
+ of all such substrings is a central step in many analyses of DNA
+ sequence. JELLYFISH can count k-mers using an order of magnitude less
+ memory and an order of magnitude faster than other k-mer counting
+ packages by using an efficient encoding of a hash table and by
+ exploiting the compare-and-swap CPU instruction to increase
+ parallelism.
+ .
+ JELLYFISH is a command-line program that reads FASTA and multi-FASTA
+ files containing DNA sequences. It outputs its k-mer counts in an
+ binary format, which can be translated into a human-readable text
+ format using the jellyfish dump command.
+ .
+ If you use JELLYFISH in your research, please cite:
+ Guillaume Marcais and Carl Kingsford, A fast, lock-free approach for
+ efficient parallel counting of occurrences of k-mers. Bioinformatics
+ (2011) 27(6): 764-770 (first published online January 7, 2011)
+ doi:10.1093/bioinformatics/btr011
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 000..4e4870f
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,42 @@
+Format: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=filerev=174
+Upstream-Name: JELLYFISH
+Upstream-Contact: Guillaume Marçais gmarc...@umd.edu
+Source: http://www.cbcb.umd.edu/software/jellyfish/
+
+Files: *
+Copyright: Copyright 2011 Guillaume Marçais1, Carl Kingsford
+License: GPL-3+
+ See `/usr/share/common-licenses/GPL'.
+
+Files: randomc.h
+Copyright: Copyright 2008 Agner Fog
+License: GPL
+ See `/usr/share/common-licenses/GPL'.
+
+Files: half.h
+Copyright: Copyright 2002, Industrial Light Magic
+License:
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions
+ are met:
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following
+ disclaimer in the documentation and/or other materials provided
+ with the distribution.
+ * Neither the name of Industrial Light Magic nor the names of
+ its contributors may be used to endorse or promote products derived
+ from this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ AS IS AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 000..64b0214
--- /dev/null
+++ b/debian/docs
@@ -0,0 +1,2 @@
+README
+doc/jellyfish.pdf
diff --git a/debian/install b/debian/install
new file mode 100644
index 000..e772481
--- /dev/null
+++ b/debian/install
@@ -0,0 +1 @@
+usr/bin
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 000..c7a2ecf
--- /dev
[med-svn] [SCM] jellyfish annotated tag, upstream/1.1.2, created. upstream/1.1.2
The annotated tag, upstream/1.1.2 has been created at 3ae3d0681c314eda00ebdf430bed9d58f0a06753 (tag) tagging 50f2f49253b432acdb224e4cc94ce856c4d6991a (commit) tagged by Shaun Jackman on Mon Oct 10 11:33:22 2011 -0700 - Shortlog Upstream version 1.1.2 Shaun Jackman (1): Imported Upstream version 1.1.2 --- -- count k-mers of DNA ___ 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] [SCM] jellyfish branch, pristine-tar, created. 0fb0e92af013dd85e336476e91296f865f677b65
The branch, pristine-tar has been created at 0fb0e92af013dd85e336476e91296f865f677b65 (commit) - Shortlog commit 0fb0e92af013dd85e336476e91296f865f677b65 Author: Shaun Jackman sjack...@gmail.com Date: Mon Oct 10 11:33:22 2011 -0700 pristine-tar data for jellyfish_1.1.2.orig.tar.gz --- -- count k-mers of DNA ___ 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] [SCM] jellyfish branch, upstream, created. upstream/1.1.2
The branch, upstream has been created at 50f2f49253b432acdb224e4cc94ce856c4d6991a (commit) - Shortlog --- -- count k-mers of DNA ___ 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] [SCM] jellyfish tag, debian/1.1.2-1, created. upstream/1.1.2-1-g6529ac1
The tag, debian/1.1.2-1 has been created at 6529ac1a2916faf781c227cd16dfab240bc57611 (commit) - Shortlog commit 6529ac1a2916faf781c227cd16dfab240bc57611 Author: Shaun Jackman sjack...@gmail.com Date: Mon Oct 10 14:04:37 2011 -0700 Initial release. --- -- count k-mers of DNA ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
Accepted gmap 2011-09-14-1 (source i386)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Thu, 15 Sep 2011 14:36:34 -0700 Source: gmap Binary: gmap Architecture: source i386 Version: 2011-09-14-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: gmap - spliced and SNP-tolerant alignment for mRNA and short reads Changes: gmap (2011-09-14-1) unstable; urgency=low . * New upstream release. Checksums-Sha1: f4c32a863e6b0a5cc632555b49fc903328ce87fb 1272 gmap_2011-09-14-1.dsc f30edf033273ba7e8ab9df50576d2b6b197648b6 3366990 gmap_2011-09-14.orig.tar.gz 48a36871262b8a48880527eff7faed0c40f2eeb4 11271 gmap_2011-09-14-1.debian.tar.gz da25868a21a7f28fa9c13bbd1bb19405e0a37bdc 6388954 gmap_2011-09-14-1_i386.deb Checksums-Sha256: 6c7e11da4cbfc6f5f2ffadeec8825514651354ab478966348ec97a6cc02f0a39 1272 gmap_2011-09-14-1.dsc d4d156a965672e5ba844ccb20c8f1a58f1b0d925bb9d6168b06ab68982619411 3366990 gmap_2011-09-14.orig.tar.gz efb7fdd8f89bb5630252c8883a305c9e3ec574e9e5f0111f625efc42f215324b 11271 gmap_2011-09-14-1.debian.tar.gz 27d727e08963be9aa55e0b57aa645b5ed93cdd02802f5ba41327712f45b9f6b4 6388954 gmap_2011-09-14-1_i386.deb Files: 0059ea566a2265408de59119cc445e5f 1272 non-free/science optional gmap_2011-09-14-1.dsc 95e0734f50a15c1aae4520322c1fdbe2 3366990 non-free/science optional gmap_2011-09-14.orig.tar.gz bef3445e9505959ec8b33ff5b9e0214b 11271 non-free/science optional gmap_2011-09-14-1.debian.tar.gz be8d2b412d099fdc4090d9c17f79cbf4 6388954 non-free/science optional gmap_2011-09-14-1_i386.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAk5ycVUACgkQvFdYF1IwUUq2YQCgrsDjYS0Vx0dHwCFRFdrzvsQf kN8Ani3IJjvwO+QCxIB+2OFNyySDyY6s =ge68 -END PGP SIGNATURE- Accepted: gmap_2011-09-14-1.debian.tar.gz to non-free/g/gmap/gmap_2011-09-14-1.debian.tar.gz gmap_2011-09-14-1.dsc to non-free/g/gmap/gmap_2011-09-14-1.dsc gmap_2011-09-14-1_i386.deb to non-free/g/gmap/gmap_2011-09-14-1_i386.deb gmap_2011-09-14.orig.tar.gz to non-free/g/gmap/gmap_2011-09-14.orig.tar.gz -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1r4jmv-0002tm...@franck.debian.org
[med-svn] [SCM] gmap branch, master, updated. upstream/2011-09-09-25-g2d7fb22
The following commit has been merged in the master branch: commit 6d902e0e8aae3db3b68fb16608fd242426196e59 Merge: ce800895fb3da208229f877b5e8025fd72d80ae2 2ab08afc5f80572c59ddf6bde8222aa65ee41ab2 Author: Shaun Jackman sjack...@debian.org Date: Thu Sep 15 14:36:32 2011 -0700 Merge commit 'upstream/2011-09-14' -- Align mRNA and EST sequences to a genome ___ 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] [SCM] gmap branch, master, updated. upstream/2011-09-09-25-g2d7fb22
The following commit has been merged in the master branch: commit 2d7fb22fd04e815078965cd2e7827bc7ae82cc67 Author: Shaun Jackman sjack...@debian.org Date: Thu Sep 15 14:43:17 2011 -0700 New upstream release. diff --git a/debian/changelog b/debian/changelog index e8cfaf8..c348c40 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +gmap (2011-09-14-1) unstable; urgency=low + + * New upstream release. + + -- Shaun Jackman sjack...@debian.org Thu, 15 Sep 2011 14:36:34 -0700 + gmap (2011-09-09-1) unstable; urgency=low * New upstream release. @@ -33,7 +39,7 @@ gmap (2010-07-21-1) unstable; urgency=low gmap (2010-07-20-1) unstable; urgency=low * New upstream release. - * Bump Standards-Version to 3.9.0. + * Bump Standards-Version to 3.9.0. -- Shaun Jackman sjack...@debian.org Wed, 21 Jul 2010 11:07:28 -0700 -- Align mRNA and EST sequences to a genome ___ 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] [SCM] gmap annotated tag, upstream/2011-09-14, created. upstream/2011-09-14
The annotated tag, upstream/2011-09-14 has been created at 641e76314761451bd0d32600d3d2cfde27c72c13 (tag) tagging 2ab08afc5f80572c59ddf6bde8222aa65ee41ab2 (commit) replaces upstream/2011-09-09 tagged by Shaun Jackman on Thu Sep 15 14:36:32 2011 -0700 - Shortlog Upstream version 2011-09-14 Shaun Jackman (1): Imported Upstream version 2011-09-14 --- -- Align mRNA and EST sequences to a genome ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
Accepted gmap 2011-09-09-1 (source i386)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Wed, 14 Sep 2011 17:09:21 -0700 Source: gmap Binary: gmap Architecture: source i386 Version: 2011-09-09-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: gmap - spliced and SNP-tolerant alignment for mRNA and short reads Changes: gmap (2011-09-09-1) unstable; urgency=low . * New upstream release. Checksums-Sha1: fee2c5b42e7b1b60246ebbc62a9e23454f165d35 1272 gmap_2011-09-09-1.dsc a2a3a4e43ce69ee646918d06087dc0c2dd2fca00 3366072 gmap_2011-09-09.orig.tar.gz ac5f872d644be75d59fb6ca95e236f5502890e88 11274 gmap_2011-09-09-1.debian.tar.gz fbfe19f050b0189eb043a3da187039dea8e47f4b 6388454 gmap_2011-09-09-1_i386.deb Checksums-Sha256: bda3f4651ff9c347ee48365ad10f0c6ccb15c688fec7d3aaabf84c634c81ab86 1272 gmap_2011-09-09-1.dsc a890316da08e3abd70768336564c2e9db4cd822780ac150040626244b69a529d 3366072 gmap_2011-09-09.orig.tar.gz 90937d9d67fcbb1fdb48730b72c8af6cdce575dac84991e6738ccae0a3440b18 11274 gmap_2011-09-09-1.debian.tar.gz 250380d39a5907028471836f051d95582d4a01a2966b3e997a3b8f8e7170d5b1 6388454 gmap_2011-09-09-1_i386.deb Files: 8403a35b42631f7b5c5967e0b511f19f 1272 non-free/science optional gmap_2011-09-09-1.dsc 61ec0aa47452b74fe584c11422d340fd 3366072 non-free/science optional gmap_2011-09-09.orig.tar.gz 010e05bd1f3c43d319b12796d625418e 11274 non-free/science optional gmap_2011-09-09-1.debian.tar.gz dffd6b68156ec1dc8a9ea0c05d8cb176 6388454 non-free/science optional gmap_2011-09-09-1_i386.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAk5xSjYACgkQvFdYF1IwUUplQgCfaXKm4tQLiDPteUvTviBj4WyP NLsAoMDEMB8hgfmECxhOavfmGmqMNVW1 =+yCS -END PGP SIGNATURE- Accepted: gmap_2011-09-09-1.debian.tar.gz to non-free/g/gmap/gmap_2011-09-09-1.debian.tar.gz gmap_2011-09-09-1.dsc to non-free/g/gmap/gmap_2011-09-09-1.dsc gmap_2011-09-09-1_i386.deb to non-free/g/gmap/gmap_2011-09-09-1_i386.deb gmap_2011-09-09.orig.tar.gz to non-free/g/gmap/gmap_2011-09-09.orig.tar.gz -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1r406i-0008jz...@franck.debian.org
[med-svn] [SCM] gmap branch, master, updated. upstream/2011-08-15-23-gce80089
The following commit has been merged in the master branch: commit e7e10a2c7b4941e79bd3703532cee5c83d6df0a3 Merge: e21796d88ba8cf78ddbb3c851e412329ee96b25b a50c159e265f15a53ab51ddc19ee77962be73a4f Author: Shaun Jackman sjack...@debian.org Date: Wed Sep 14 17:08:07 2011 -0700 Merge commit 'upstream/2011-09-09' -- Align mRNA and EST sequences to a genome ___ 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] [SCM] gmap branch, master, updated. upstream/2011-08-15-23-gce80089
The following commit has been merged in the master branch: commit ce800895fb3da208229f877b5e8025fd72d80ae2 Author: Shaun Jackman sjack...@debian.org Date: Wed Sep 14 17:44:09 2011 -0700 New upstream release. diff --git a/debian/changelog b/debian/changelog index c3c12ac..e8cfaf8 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,9 @@ +gmap (2011-09-09-1) unstable; urgency=low + + * New upstream release. + + -- Shaun Jackman sjack...@debian.org Wed, 14 Sep 2011 17:09:21 -0700 + gmap (2011-08-15-1) unstable; urgency=low * New upstream release. diff --git a/debian/gmap.1 b/debian/gmap.1 index 6a89b8e..dc1d6a8 100644 --- a/debian/gmap.1 +++ b/debian/gmap.1 @@ -29,7 +29,15 @@ built explicitly during setup), not compressed version .TP \fB\-g\fR, \fB\-\-gseg\fR=\fIfilename\fR -User\-suppled genomic segment +User-supplied genomic segment +.TP +\fB-2\fR, \fB--pairalign\fR +Align two sequences in FASTA format via stdin, first one being +genomic and second one being cDNA +.TP +\fB--cmdline\fR=\fISTRING\fR,\fISTRING\fR +Align these two sequences provided on the command line, +first one being genomic and second one being cDNA .TP \fB\-q\fR, \fB\-\-part\fR=\fIINT\fR/\fIINT\fR Process only the i-th out of every n sequences @@ -55,6 +63,10 @@ Note: For a single sequence, all data structures use mmap. If mmap not available and allocate not chosen, then will use fileio (very slow) .TP +\fB--nosplicing\fR +Turns off splicing (useful for aligning genomic sequences +onto a genome) +.TP \fB-K\fR, \fB--intronlength\fR=\fIINT\fR Max length for one internal intron (default 100) .TP @@ -100,6 +112,10 @@ high\-identity sequences and high reward otherwise Allow an insertion and deletion close to each other (0=no, 1=yes (default), 2=only for high-quality alignments) .TP +\fB--microexon-spliceprob\fR=\fIFLOAT\fR +Allow microexons only if one of the splice site probabilities is +greater than this value (default 0.90) +.TP \fB\-p\fR, \fB\-\-prunelevel\fR Pruning level: 0=no pruning (default), 1=poor seqs, 2=repetitive seqs, 3=poor and repetitive diff --git a/debian/gsnap.1 b/debian/gsnap.1 index 12ebb94..0578686 100644 --- a/debian/gsnap.1 +++ b/debian/gsnap.1 @@ -37,6 +37,21 @@ Amount of barcode to remove from start of read (default 0) Orientation of paired-end reads Allowed values: FR (fwd-rev, or typical Illumina; default), FR (rev-fwd, for circularized inserts), or FF (fwd-fwd, same strand) +.TP +\fB--fastq-id-start\fR=\fIINT\fR +Starting position of identifier in FASTQ header, space-delimited (= 1) +.TP +\fB--fastq-id-end\fR=\fIINT\fR +Ending position of identifier in FASTQ header, space-delimited (= 1) + Examples: + @HWUSI-EAS100R:6:73:941:1973#0/1 start=1, end=1 (default) + @SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36 + start=1, end=1 + = identifier is SRR001666.1 + start=2, end=2 + = identifier is 071112_SLXA-EAS1_s_7:5:1:817:345 + start=1, end=2 + = identifier is SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 .SS Computation options .PP @@ -76,6 +91,11 @@ Whether to count unknown (N) characters in the query as a mismatch Whether to count unknown (N) characters in the genome as a mismatch (0=no, 1=yes (default)) .TP +\fB--terminal-threshold\fR=\fIINT\fR +Threshold for searching for a terminal alignment (from one end of the +read to the best possible position at the other end) (default 3). +To turn off terminal alignments, set this to a high value. +.TP \fB\-i\fR, \fB\-\-indel\-penalty\fR=\fIINT\fR Penalty for an indel (default 2). Counts against mismatches allowed. To find indels, make @@ -101,15 +121,6 @@ Maximum number of end deletions allowed (default 6) Report suboptimal hits beyond best hit (default 0) All hits with best score plus suboptimal-levels are reported .TP -\fB\-R\fR, \fB\-\-masking\fR=\fIINT\fR -Masking of frequent/repetitive oligomers to avoid spending time -on non\-unique or repetitive reads - 0 = no masking (will try to find non\-unique or repetitive matches) - 1 = mask frequent oligomers - 2 = mask frequent and repetitive oligomers (fastest) (default) - 3 = greedy frequent: mask frequent oligomers first, then try no masking if alignments not found - 4 = greedy repetitive: mask frequent and repetitive oligomers first, then try no masking if alignments not found -.TP \fB-a\fR, \fB--adapter-strip\fR=\fISTRING\fR Method for removing adapters from reads. Currently allowed values: off, paired. @@ -143,7 +154,8 @@ Alignment mode: standard (default), cmet, or atoi .TP \fB--tallydir\fR=\fISTRING\fR Directory for tally IIT file to resolve concordant multiple results -(default is location of genome index files specified using -D and -d) +(default is location of genome index files specified using -D and -d). +Note: can just give full path name to --use\-tally instead. .TP \fB--use-tally\fR=\fISTRING\fR Use this tally IIT file to resolve concordant multiple results @@ -151,7 +163,8 @@ Use this tally IIT file to resolve
[med-svn] [SCM] gmap branch, pristine-tar, updated. 494d0320cfdb45911699db2569175950eb7323d5
The following commit has been merged in the pristine-tar branch: commit 494d0320cfdb45911699db2569175950eb7323d5 Author: Shaun Jackman sjack...@debian.org Date: Wed Sep 14 17:08:07 2011 -0700 pristine-tar data for gmap_2011-09-09.orig.tar.gz diff --git a/gmap_2011-09-09.orig.tar.gz.delta b/gmap_2011-09-09.orig.tar.gz.delta new file mode 100644 index 000..440921b Binary files /dev/null and b/gmap_2011-09-09.orig.tar.gz.delta differ diff --git a/gmap_2011-09-09.orig.tar.gz.id b/gmap_2011-09-09.orig.tar.gz.id new file mode 100644 index 000..eb19da4 --- /dev/null +++ b/gmap_2011-09-09.orig.tar.gz.id @@ -0,0 +1 @@ +a50c159e265f15a53ab51ddc19ee77962be73a4f -- Align mRNA and EST sequences to a genome ___ 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] [SCM] gmap annotated tag, upstream/2011-09-09, created. upstream/2011-09-09
The annotated tag, upstream/2011-09-09 has been created at f15661026d0ca5f7e875bc0196921a3863fc28a1 (tag) tagging a50c159e265f15a53ab51ddc19ee77962be73a4f (commit) replaces upstream/2011-08-15 tagged by Shaun Jackman on Wed Sep 14 17:08:07 2011 -0700 - Shortlog Upstream version 2011-09-09 Shaun Jackman (1): Imported Upstream version 2011-09-09 --- -- Align mRNA and EST sequences to a genome ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
Accepted abyss 1.3.0-1 (source amd64)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Sun, 11 Sep 2011 10:00:13 -0700 Source: abyss Binary: abyss Architecture: source amd64 Version: 1.3.0-1 Distribution: unstable Urgency: low Maintainer: Shaun Jackman sjack...@debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: abyss - de novo, parallel, sequence assembler for short reads Changes: abyss (1.3.0-1) unstable; urgency=low . * New upstream release. * Add libboost-graph-dev to Build-Depends. Checksums-Sha1: 60ae5222605e58f9fb0a4db7d0a7d6ee09329e0e 1107 abyss_1.3.0-1.dsc ca067e7b94329f3e0be764a447e77389d94f4b40 509670 abyss_1.3.0.orig.tar.gz 7351712296e33361cd7138ef9491d2e5c7f77b9d 8763 abyss_1.3.0-1.debian.tar.gz 926b173343f994949cae604fef02818f67260bf8 1237914 abyss_1.3.0-1_amd64.deb Checksums-Sha256: dded04ce00689614d9ba8529b872cd4718ead06301e3ae8bc4a647fafede105d 1107 abyss_1.3.0-1.dsc 50ea7d29f442060fa9cb9f794e5b651d99ced38049be3a489c9bbe37288e8012 509670 abyss_1.3.0.orig.tar.gz 492dceabf411db8b8b152e9afabae23240ba6e446042bfe1223373142a2f837e 8763 abyss_1.3.0-1.debian.tar.gz df63a9bf84683067fd49559b197a1b36d7d3c5beee1ec9c0e8e8470856ad35cd 1237914 abyss_1.3.0-1_amd64.deb Files: efa08ddcabd7fdb3d206860630dc67fd 1107 non-free/science optional abyss_1.3.0-1.dsc 90f94198fef8c6abc70cafd57018023d 509670 non-free/science optional abyss_1.3.0.orig.tar.gz 29781d5f7b5b500c6e01f2e6ac462bc7 8763 non-free/science optional abyss_1.3.0-1.debian.tar.gz dbb990fffa8b1d890ad64777cd1bcb01 1237914 non-free/science optional abyss_1.3.0-1_amd64.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) iEYEARECAAYFAk5tEJMACgkQvFdYF1IwUUr4JQCgt6QE8nfRGl1mnofb4be85t/5 /gQAoKM0DyF5RUG2Yab3zqkJXQTMsKtb =DWwK -END PGP SIGNATURE- Accepted: abyss_1.3.0-1.debian.tar.gz to non-free/a/abyss/abyss_1.3.0-1.debian.tar.gz abyss_1.3.0-1.dsc to non-free/a/abyss/abyss_1.3.0-1.dsc abyss_1.3.0-1_amd64.deb to non-free/a/abyss/abyss_1.3.0-1_amd64.deb abyss_1.3.0.orig.tar.gz to non-free/a/abyss/abyss_1.3.0.orig.tar.gz -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1r2qvu-0005fo...@franck.debian.org
Accepted gmap 2011-08-15-1 (source i386)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Tue, 23 Aug 2011 10:45:46 -0700 Source: gmap Binary: gmap Architecture: source i386 Version: 2011-08-15-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: gmap - spliced and SNP-tolerant alignment for mRNA and short reads Changes: gmap (2011-08-15-1) unstable; urgency=low . * New upstream release. * Bump Standards-Version to 3.9.2. Checksums-Sha1: b1f82ee1e343268850d2f719705ac16959981713 1272 gmap_2011-08-15-1.dsc e5bd9258e564c51d95042097207105b4b0507209 3356627 gmap_2011-08-15.orig.tar.gz c4d69df612da6dd47bdd271160fc9a7aec5959d3 10724 gmap_2011-08-15-1.debian.tar.gz 2a8971f8e4c035ebcc4b889a38800cefce251605 6375422 gmap_2011-08-15-1_i386.deb Checksums-Sha256: 0ed55b35830f0d18693e5fa325a8985a4c3072dbbd0a0a84bf297f4e50bc1f81 1272 gmap_2011-08-15-1.dsc bf61cb435e31919dc5fd451099f62510a7b37fe214600343efbe1be82890dbbe 3356627 gmap_2011-08-15.orig.tar.gz 2ef0d95393c6e9a08c66da35d1aa3db5395c0196d91522eb3c9df2d4b883ca28 10724 gmap_2011-08-15-1.debian.tar.gz 71ee4842d093f7d125ab793b8a5db6c804a8753d604187a18d0e22a9a8a7411b 6375422 gmap_2011-08-15-1_i386.deb Files: 3fb417d43054b48a1d7c7d833684caa3 1272 non-free/science optional gmap_2011-08-15-1.dsc e57e5a183fe7104c5f20a57ef6fa4c36 3356627 non-free/science optional gmap_2011-08-15.orig.tar.gz c6afaf4e68278dca83774096a1b2b32b 10724 non-free/science optional gmap_2011-08-15-1.debian.tar.gz 44f3d4ab55374a21cb00fced0677972b 6375422 non-free/science optional gmap_2011-08-15-1_i386.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAk5UITsACgkQvFdYF1IwUUphMwCgj3SeRJYgmJesMQQzeYAOh0ii nTEAoMceh6htEXPqCub2tueFewTHuoa0 =BrzC -END PGP SIGNATURE- Accepted: gmap_2011-08-15-1.debian.tar.gz to non-free/g/gmap/gmap_2011-08-15-1.debian.tar.gz gmap_2011-08-15-1.dsc to non-free/g/gmap/gmap_2011-08-15-1.dsc gmap_2011-08-15-1_i386.deb to non-free/g/gmap/gmap_2011-08-15-1_i386.deb gmap_2011-08-15.orig.tar.gz to non-free/g/gmap/gmap_2011-08-15.orig.tar.gz -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1qvzhx-ae...@franck.debian.org
[med-svn] [SCM] gmap branch, master, updated. upstream/2011-03-11-21-ge21796d
The following commit has been merged in the master branch: commit 3094fe8acfc2dc083edd82725214c7e97cdc7eb6 Merge: 95ea5b7cc34322fd2106a539c605d63304554905 76e4b00922a1232a84bdf9e60525fc4c084d7eff Author: Shaun Jackman sjack...@debian.org Date: Tue Aug 23 14:34:57 2011 -0700 Merge commit 'upstream/2011-08-15' -- Align mRNA and EST sequences to a genome ___ 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] [SCM] gmap branch, master, updated. upstream/2011-03-11-21-ge21796d
The following commit has been merged in the master branch: commit e21796d88ba8cf78ddbb3c851e412329ee96b25b Author: Shaun Jackman sjack...@debian.org Date: Tue Aug 23 14:54:38 2011 -0700 New upstream release. diff --git a/debian/changelog b/debian/changelog index 9cb0e8c..c3c12ac 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +gmap (2011-08-15-1) unstable; urgency=low + + * New upstream release. + * Bump Standards-Version to 3.9.2. + + -- Shaun Jackman sjack...@debian.org Tue, 23 Aug 2011 10:45:46 -0700 + gmap (2011-03-11-1) unstable; urgency=low * New upstream release. diff --git a/debian/control b/debian/control index 12fa327..c11fbfd 100644 --- a/debian/control +++ b/debian/control @@ -5,7 +5,7 @@ Maintainer: Debian Med Packaging Team debian-med-packaging@lists.alioth.debian. DM-Upload-Allowed: yes Uploaders: Shaun Jackman sjack...@debian.org Build-Depends: debhelper (= 7.0.50~), autotools-dev -Standards-Version: 3.9.1 +Standards-Version: 3.9.2 Homepage: http://research-pub.gene.com/gmap/ Vcs-Git: git://git.debian.org/git/debian-med/gmap.git Vcs-Browser: http://git.debian.org/?p=debian-med/gmap.git diff --git a/debian/copyright b/debian/copyright index 23f323b..465e2a2 100644 --- a/debian/copyright +++ b/debian/copyright @@ -3,7 +3,7 @@ Name: GMAP Maintainer: Thomas Wu t...@gene.com, Colin K. Watanabe c...@gene.com Source: http://research-pub.gene.com/gmap/ -Copyright: 2005 Genentech, Inc. +Copyright: 2011 Genentech, Inc. License: other Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the @@ -43,7 +43,7 @@ License: LGPL-2.1+ See `/usr/share/common-licenses/LGPL'. Files: debian/* -Copyright: 2010 Shaun Jackman sjack...@debian.org +Copyright: 2011 Shaun Jackman sjack...@debian.org License: ISC Permission to use, copy, modify, and/or distribute this software for any purpose with or without fee is hereby granted, provided that the above diff --git a/debian/gmap.1 b/debian/gmap.1 index aa488f0..6a89b8e 100644 --- a/debian/gmap.1 +++ b/debian/gmap.1 @@ -1,4 +1,4 @@ -.TH GMAP 1 Mar 2011 GMAP 2011-03-11 User Commands +.TH GMAP 1 August 2011 GMAP 2011-08-15 User Commands .SH NAME gmap \- Genomic Mapping and Alignment Program .SH SYNOPSIS @@ -18,6 +18,11 @@ Genome directory Genome database. If argument is '?' (with the quotes), this command lists available databases. .TP +\fB-k\fR, \fB--kmer\fR=\fIINT\fR +kmer size to use in genome database (allowed values: 12-15). If not +specified, the program will find the highest available kmer size in +the genome database +.TP \fB\-G\fR, \fB\-\-genomefull\fR Use full genome (all ASCII chars allowed; built explicitly during setup), not @@ -44,28 +49,32 @@ Computation options 2 allocate mmap preload mmap preload (default) 3 allocate allocatemmap preload 4 allocate allocateallocate + 5 expandallocateallocate Note: For a single sequence, all data structures use mmap. -If mmap not available and allocate not chosen, then will use fileio (slow) +If mmap not available and allocate not chosen, then will use fileio +(very slow) +.TP +\fB-K\fR, \fB--intronlength\fR=\fIINT\fR +Max length for one internal intron (default 100) .TP -\fB\-K\fR, \fB\-\-intronlength\fR=\fIINT\fR -Max length for one intron (default 100) +\fB-w\fR, \fB--localsplicedist\fR=\fIINT\fR +Max length for known splice sites at ends of sequence (default 20) .TP \fB\-L\fR, \fB\-\-totallength\fR=\fIINT\fR Max total intron length (default 240) .TP \fB\-x\fR, \fB\-\-chimera-margin\fR=\fIINT\fR Amount of unaligned sequence that triggers -search for a chimera (default off) +search for the remaining sequence (default 40). +Enables alignment of chimeric reads, and may help +with some non-chimeric reads. To turn off, set to 0. .TP \fB\-t\fR, \fB\-\-nthreads\fR=\fIINT\fR Number of worker threads .TP -\fB\-s\fR, \fB\-\-altstrain\fR -Search alternate strains in addition -.TP \fB\-C\fR, \fB\-\-chrsubsetfile\fR=\fIfilename\fR -User\-suppled chromosome subset file +User\-supplied chromosome subset file .TP \fB\-c\fR, \fB\-\-chrsubset\fR=\fIstring\fR Chromosome subset to search @@ -78,11 +87,19 @@ sense_filter, antisense_filter, or auto (default)) Trim end exons with fewer than given number of matches (in nt, default 12) .TP -\fB\-X\fR, \fB\-\-canonical\fR=\fIINT\fR -Reward for canonical and semi\-canonical introns +\fB--cross-species\fR +For cross-species alignments, use a more sensitive search for +canonical splicing +.TP +\fB--canonical-mode\fR=\fIINT\fR +Reward for canonical and semi-canonical introns 0=low reward, 1=high reward (default), 2=low reward for high\-identity sequences and high reward otherwise .TP +\fB--allow-close-indels\fR=\fIINT\fR +Allow an insertion and deletion close to each other +(0=no, 1=yes (default), 2=only for high-quality
[med-svn] [SCM] gmap annotated tag, upstream/2011-08-15, created. upstream/2011-08-15
The annotated tag, upstream/2011-08-15 has been created at 1451005dcd7a0238f7d87c915f3e16b588b63840 (tag) tagging 76e4b00922a1232a84bdf9e60525fc4c084d7eff (commit) replaces upstream/2011-03-11 tagged by Shaun Jackman on Tue Aug 23 14:34:56 2011 -0700 - Shortlog Upstream version 2011-08-15 Shaun Jackman (1): Imported Upstream version 2011-08-15 --- -- Align mRNA and EST sequences to a genome ___ 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] [SCM] gmap branch, pristine-tar, created. 126fe8513e7f2cf69b4b90e980a4425a364f94c1
The branch, pristine-tar has been created at 126fe8513e7f2cf69b4b90e980a4425a364f94c1 (commit) - Shortlog commit 126fe8513e7f2cf69b4b90e980a4425a364f94c1 Author: Shaun Jackman sjack...@debian.org Date: Tue Aug 23 14:34:56 2011 -0700 pristine-tar data for gmap_2011-08-15.orig.tar.gz --- -- Align mRNA and EST sequences to a genome ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
Accepted abyss 1.2.7-3 (source amd64)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Mon, 15 Aug 2011 11:07:19 -0700 Source: abyss Binary: abyss Architecture: source amd64 Version: 1.2.7-3 Distribution: unstable Urgency: low Maintainer: Shaun Jackman sjack...@debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: abyss - de novo, parallel, sequence assembler for short reads Changes: abyss (1.2.7-3) unstable; urgency=low . * Align/Aligner.cpp, Scaffold/scaffold.cc: Fix FTBFS bug for GCC 4.6. Checksums-Sha1: 6f0b09f20bc3ae2f5b014879cd563befbc1ae563 1087 abyss_1.2.7-3.dsc 93669233b0a7545f4d9dd3eccbc52857751e555f 8516 abyss_1.2.7-3.debian.tar.gz 8654f3f3f20e7d3c75d08c25654e1e6dc0995946 1015052 abyss_1.2.7-3_amd64.deb Checksums-Sha256: 1d7382832b0de7af5bb715699338edb662098e28e103ed52cca1f3e0bbcb2def 1087 abyss_1.2.7-3.dsc 97e496731dc7912625aa754007ba69ebadfbd513281541b5a46b1aa63a502152 8516 abyss_1.2.7-3.debian.tar.gz 8a1cc055b6f9e24c0dcee76935e6536ceddd8b6552c8009c3c3584578b74f858 1015052 abyss_1.2.7-3_amd64.deb Files: d9c6da6fbe90e91a88bcd9ce42e78729 1087 non-free/science optional abyss_1.2.7-3.dsc 085ec2fe44eaa06d742a81fa701cf0fc 8516 non-free/science optional abyss_1.2.7-3.debian.tar.gz d60ac5389f09f8f6a07b4eac51126cfb 1015052 non-free/science optional abyss_1.2.7-3_amd64.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) iEYEARECAAYFAk5JbG0ACgkQvFdYF1IwUUo7WQCfSYzU+XwU95E26JOR3R12Tc/R jx0Ani7/t+XL2oVbYLvIX7T5y106R164 =OWZo -END PGP SIGNATURE- Accepted: abyss_1.2.7-3.debian.tar.gz to non-free/a/abyss/abyss_1.2.7-3.debian.tar.gz abyss_1.2.7-3.dsc to non-free/a/abyss/abyss_1.2.7-3.dsc abyss_1.2.7-3_amd64.deb to non-free/a/abyss/abyss_1.2.7-3_amd64.deb -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1qt2fd-he...@franck.debian.org
Please autobuild abyss
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi, I'm the upstream and Debian maintainer of abyss, which is a bioinformatics software package. Its license is free for academic use and licensed to commercial users. The license currently reads Debian may redistribute this software package. Is that sufficient? I'm happy to make any changes that you require to the statement to include ABySS in the autobuild. I've added XS-Autobuild: yes to debian/control. Thanks, Shaun -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAk5ECh8ACgkQvFdYF1IwUUrGGACgwLlZaVD3B0oJ/PAYPh2WIrDz 5/UAnRssZPTYWqJKZUVJqoWgjRpECAp+ =QrKf -END PGP SIGNATURE- -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CADX6M3o4=wdxa6r100dvaanvczjm_jqrvpf8gd3ikjo6-21...@mail.gmail.com
Re: Update of the Integrative Genomics Viewer to version 2.0 ?
On 25 July 2011 17:13, Charles Plessy ple...@debian.org wrote: Le Mon, Jul 25, 2011 at 05:03:55PM -0700, Shaun Jackman a écrit : I used git-import-orig from git-buildpackage 0.5.26, but it didn't update the pristine-tar branch by default. I'll read the man page tomorrow and see if I can get it working. git-import-orig --pristine-tar :) Also, it can be made the default using a debian/gbp.conf file (example in /etc/gbp.conf). I actually recommend this, since the presence of the file reminds that the package uses git-buildpackage. Do you know how I can generate the pristine-tar data now, after I've already committed upstream/2.0.6? Trying git-import-orig --pristine-tar makes a mess of it: $ git-import-orig --pristine-tar ../2.0.6/igv_2.0.6.orig.tar.bz2 What is the upstream version? [2.0.6] gbp:info: Importing '../2.0.6/igv_2.0.6.orig.tar.bz2' to branch 'upstream'... gbp:info: Source package is igv gbp:info: Upstream version is 2.0.6 pristine-tar: committed igv_2.0.6.orig.tar.bz2.delta to branch pristine-tar fatal: tag 'upstream/2.0.6' already exists gbp:error: git returned 128 gbp:error: Couldn't tag upstream/2.0.6 gbp:error: Import of ../2.0.6/igv_2.0.6.orig.tar.bz2 failed Cheers, Shaun -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CADX6M3r1jXCAuXeVN-LV+u9Lds=Zy+T1TT=q80mudrpd+wm...@mail.gmail.com
Re: Update of the Integrative Genomics Viewer to version 2.0 ?
On 26 July 2011 10:02, Shaun Jackman sjack...@gmail.com wrote: On 25 July 2011 17:13, Charles Plessy ple...@debian.org wrote: Le Mon, Jul 25, 2011 at 05:03:55PM -0700, Shaun Jackman a écrit : I used git-import-orig from git-buildpackage 0.5.26, but it didn't update the pristine-tar branch by default. I'll read the man page tomorrow and see if I can get it working. git-import-orig --pristine-tar :) Also, it can be made the default using a debian/gbp.conf file (example in /etc/gbp.conf). I actually recommend this, since the presence of the file reminds that the package uses git-buildpackage. Do you know how I can generate the pristine-tar data now, after I've already committed upstream/2.0.6? Trying git-import-orig --pristine-tar makes a mess of it: $ git-import-orig --pristine-tar ../2.0.6/igv_2.0.6.orig.tar.bz2 What is the upstream version? [2.0.6] gbp:info: Importing '../2.0.6/igv_2.0.6.orig.tar.bz2' to branch 'upstream'... gbp:info: Source package is igv gbp:info: Upstream version is 2.0.6 pristine-tar: committed igv_2.0.6.orig.tar.bz2.delta to branch pristine-tar fatal: tag 'upstream/2.0.6' already exists gbp:error: git returned 128 gbp:error: Couldn't tag upstream/2.0.6 gbp:error: Import of ../2.0.6/igv_2.0.6.orig.tar.bz2 failed Figured it out: pristine-tar commit ../igv_2.0.6.orig.tar.bz2 Cheers, Shaun -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/cadx6m3qceml7jti7w8ootujseg6ry5rjcuijnzjczpv6aqb...@mail.gmail.com
Accepted igv 2.0.6-1 (source all)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Mon, 25 Jul 2011 11:41:18 -0700 Source: igv Binary: igv Architecture: source all Version: 2.0.6-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: igv- Integrative Genomics Viewer Changes: igv (2.0.6-1) unstable; urgency=low . * New upstream release. * debian/control: Depend and Build-Depend on libcommons-logging-java, libhttpclient-java, libhttpcore-java, libjcommon-java and libjfreechart-java. * debian/igv.1: Update. * debian/watch: Update. Checksums-Sha1: ba206c2eb48b550ad9a5bc84f2c689952deb36e0 1621 igv_2.0.6-1.dsc cdcea0f4061431be7170772870bec80b70a3b646 5346338 igv_2.0.6.orig.tar.bz2 919cd8e06952d7cde0eaf957515538e52b133d85 17087 igv_2.0.6-1.debian.tar.gz 8dc3170cd681ddbfb1841030c48cf8583ba09350 7065738 igv_2.0.6-1_all.deb Checksums-Sha256: 0d864ac93530ed0f9b3b10664e31b6e2621ffa86f039a115e7c23ef222b72fd0 1621 igv_2.0.6-1.dsc e85f2c02f07a8d4291be30c045de0f0c96752e16dea38ceb2e3bc8d484bc523d 5346338 igv_2.0.6.orig.tar.bz2 77ab8ff7d0d2ea27bc7453770b0290aeb158c1883eee297013415f22abb47a9b 17087 igv_2.0.6-1.debian.tar.gz d10374297ab80f735c78d62606a7db64ac10303f216554ab275a1d3bca0eccf9 7065738 igv_2.0.6-1_all.deb Files: 5920780ddf8a4f0dedd55c9140c54b5d 1621 non-free/science optional igv_2.0.6-1.dsc 1c7db223f64ae52f6e2cc53bfc54a163 5346338 non-free/science optional igv_2.0.6.orig.tar.bz2 6f2dce1b64cbb94640814b7e9a00d9a8 17087 non-free/science optional igv_2.0.6-1.debian.tar.gz 4751c1cb151b7dc837258b2e2ef8fe51 7065738 non-free/science optional igv_2.0.6-1_all.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAk4tx8UACgkQvFdYF1IwUUoXywCgxrpHMDjYl8mgc+N0rMRJCN57 Ng8AoOfNLF2IPgxHKt2/qSG1ZiJzNt4k =qi4h -END PGP SIGNATURE- Accepted: igv_2.0.6-1.debian.tar.gz to non-free/i/igv/igv_2.0.6-1.debian.tar.gz igv_2.0.6-1.dsc to non-free/i/igv/igv_2.0.6-1.dsc igv_2.0.6-1_all.deb to non-free/i/igv/igv_2.0.6-1_all.deb igv_2.0.6.orig.tar.bz2 to non-free/i/igv/igv_2.0.6.orig.tar.bz2 -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1qls4a-0002z7...@franck.debian.org
Accepted abyss 1.2.7-2 (source i386)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Thu, 21 Jul 2011 09:55:52 -0700 Source: abyss Binary: abyss Architecture: source i386 Version: 1.2.7-2 Distribution: unstable Urgency: low Maintainer: Shaun Jackman sjack...@debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: abyss - de novo, parallel, sequence assembler for short reads Changes: abyss (1.2.7-2) unstable; urgency=low . * debian/control: Add `XS-Autobuild: yes'. Suggest openmpi-bin. * debian/copyright: Change `Format-Specification' to `Format'. Checksums-Sha1: 3ef578f54afb50e04d983ae56fb81ff169b86d87 1087 abyss_1.2.7-2.dsc 13dae318af219761d62b293ce9e0d99646505ecb 8239 abyss_1.2.7-2.debian.tar.gz 2733de736c91c15bf8c6e8c0567f880eb123b747 970106 abyss_1.2.7-2_i386.deb Checksums-Sha256: 7883389cc726dfef2796028e05d4dc1df809072c42cf26be5a0f35ffcc0b6e26 1087 abyss_1.2.7-2.dsc 66ab2c089da6e336574699a142a30a9acb8ba9802d4413a0a069b2b30d5dd2ff 8239 abyss_1.2.7-2.debian.tar.gz 4e14e09f78984c25cea4ddcaec61bb775665daf4b81c14849a3a0d14991d38e3 970106 abyss_1.2.7-2_i386.deb Files: 88e486a8dc10dbba702315e3d4b75b6a 1087 non-free/science optional abyss_1.2.7-2.dsc 22922dc37323a3bbf37c239107ab5fed 8239 non-free/science optional abyss_1.2.7-2.debian.tar.gz 194016527071936d4336447bcb054b6f 970106 non-free/science optional abyss_1.2.7-2_i386.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAk4t4lYACgkQvFdYF1IwUUqODQCfVbZSgLn1DrHHua1dFg+uS1Pc bnwAn3ay1iOL9ZA45xJwETIHBWppaXBW =2NMi -END PGP SIGNATURE- Accepted: abyss_1.2.7-2.debian.tar.gz to non-free/a/abyss/abyss_1.2.7-2.debian.tar.gz abyss_1.2.7-2.dsc to non-free/a/abyss/abyss_1.2.7-2.dsc abyss_1.2.7-2_i386.deb to non-free/a/abyss/abyss_1.2.7-2_i386.deb -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1qlt1c-0005wh...@franck.debian.org
Re: circos licensing issues
Hi all, I work with the author of Circos and am a Debian developer. I'm happy to help if you need a contact inside. Cheers, Shaun On 21 July 2011 22:33, Olivier Sallou olivier.sal...@irisa.fr wrote: Hi, I have contacted upstream author, and he will remove copyright issues on fonts in next version (that should come soon). By the way, upstream patches will contain full code, making easier to format original source code for packaging. So I propose to wait for the next version for the package. I will check it and let you know for further upload. Thanks Olivier -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (pgp.mit.edu) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438 -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/4e290bbd.7070...@irisa.fr -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/cadx6m3rpe017wcxinxezb-m1pwd1qnshrzqpdnzk25-dfsx...@mail.gmail.com
Re: Update of the Integrative Genomics Viewer to version 2.0 ?
Hi Charles, I've just uploaded IGV 2.0.6-1. What do I do with the pristine-tar and meta branches? These branches are new to me. Cheers, Shaun On 28 June 2011 10:38, Shaun Jackman sjack...@gmail.com wrote: Hi Charles, I'm going to be pretty busy for about two weeks. I probably won't have time to look into this until then. If 1.5.65 compiles cleanly and works, there's no harm in uploading that in the mean time. I can take a look into the 2.0 log4j issue two weeks from now. The RollingFileAppender class is at least present in the jar: $ strings /usr/share/java/log4j-1.2-1.2.15.jar |grep /RollingFileAppender.class$ org/apache/log4j/RollingFileAppender.class Cheers, Shaun On 27 June 2011 23:17, Charles Plessy ple...@debian.org wrote: Dear Shaun and everybody, There is a major update of the IGV, which may be interesting to follow. Unfortunately, I have tried to build it from source but could not produce a JAR file that can be executed. I have been reluctant to modify the master branch of the Git repository where we manage the igv package, as there is a version 1.5.65 on the upstream download area, but not in their changelog, which suggests that there may be some maintainance. What shall I do: share work on version 2.0 in our master branch, make a separate branch for the moment, or provide a temporary fork separately ? For the record, the error I get is: log4j:ERROR Could not find value for key log4j.appender.R log4j:ERROR Could not instantiate appender named R. ERROR [2011-06-28 15:16:26,637] [DefaultExceptionHandler.java:42] [main] Unhandled exception java.lang.NoClassDefFoundError: org/apache/log4j/RollingFileAppender at org.broad.igv.ui.Main.initializeLog(Main.java:225) at org.broad.igv.ui.Main.initApplication(Main.java:94) at org.broad.igv.ui.Main.main(Main.java:70) Caused by: java.lang.ClassNotFoundException: org.apache.log4j.RollingFileAppender at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:334) ... 3 more Have a nice day, -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CADX6M3rG7Mb0-qErugTjCZgqTd1H4u4BmSzKLWPFP3WYFO9D=q...@mail.gmail.com
Re: Update of the Integrative Genomics Viewer to version 2.0 ?
On 25 July 2011 16:12, Charles Plessy ple...@debian.org wrote: Le Mon, Jul 25, 2011 at 12:56:01PM -0700, Shaun Jackman a écrit : Hi Charles, I've just uploaded IGV 2.0.6-1. What do I do with the pristine-tar and meta branches? These branches are new to me. Hi Shaun, thanks a lot for bringing us IGV 2.0 ! the pristine-tar is a convenience branch that stores information necessary to re-create a bit-by-bit identical upstream archive (‘.orig.tar.gz’), so that it avoids problems of hashsum mismatches when uploading Debian revisions (perhaps you have seen these rejection emails on our maintainer mailing list). For some reasons, just doing ‘tar xfvz’ from the upstream branch (ignoring .git, of course) will not produce exactly the same file on different systems. The main helper tool we use to register an ‘upstream’ tarball (in the case of IGV, that is what the get-orig-source script produces) is ‘git-import-orig’ from the git-buildpackage toolkit. Hi Charles, I used git-import-orig from git-buildpackage 0.5.26, but it didn't update the pristine-tar branch by default. I'll read the man page tomorrow and see if I can get it working. Cheers, Shaun -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/CADX6M3qSPyK-rC1kU9vcNcYMy=x4me_81rg_mfnqgwjtgjm...@mail.gmail.com
Accepted abyss 1.2.7-1 (source i386)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Fri, 24 Jun 2011 12:16:36 -0700 Source: abyss Binary: abyss Architecture: source i386 Version: 1.2.7-1 Distribution: unstable Urgency: low Maintainer: Shaun Jackman sjack...@debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: abyss - de novo, parallel, sequence assembler for short reads Closes: 631534 Changes: abyss (1.2.7-1) unstable; urgency=low . * Initial release. Closes: #631534. Checksums-Sha1: da7ae372d4d7effd5ceb9df243b5c7471178a69a 1072 abyss_1.2.7-1.dsc 84708296878ef0be2c6eedcba9fbf74ade08227a 467831 abyss_1.2.7.orig.tar.gz 5f579ce3fd160a7aa16598f0aed011128196b1e7 8105 abyss_1.2.7-1.debian.tar.gz 3bbebbdd286d93a82c29ba0d6eb75341df8be8f8 969438 abyss_1.2.7-1_i386.deb Checksums-Sha256: a2bd56908e995dcbbf47d103aa0d11dbb8e61cf5e2bad794722128cf6d5d07d9 1072 abyss_1.2.7-1.dsc 2c3bc0b6046dbbfcb9298f91314c4a2979886009a5d5d68178871e3a8b1d11c2 467831 abyss_1.2.7.orig.tar.gz 2e9fc109f580913966b46c4e81d5affcb370eaf74a8bfa364c414cb8d3acf3d1 8105 abyss_1.2.7-1.debian.tar.gz 5d28924172b5c8561a2af814d2de8a4fa9bbde23ec5f4968b5278b2808898973 969438 abyss_1.2.7-1_i386.deb Files: 8737a4060736035f5385f097a046c786 1072 non-free/science optional abyss_1.2.7-1.dsc 22d95b5a50528fac7afafed9caf594ba 467831 non-free/science optional abyss_1.2.7.orig.tar.gz b1f0bf5f59f90abb235316b6e49fcf38 8105 non-free/science optional abyss_1.2.7-1.debian.tar.gz 900d2cdcb848ff182e5520b127d73a18 969438 non-free/science optional abyss_1.2.7-1_i386.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAk4E/ngACgkQvFdYF1IwUUqwhACePQVkFaU84UWuRZz6WBayJbK2 f+wAnig3wpXtnj2KyxmovTePjfuBomo4 =ciM9 -END PGP SIGNATURE- Accepted: abyss_1.2.7-1.debian.tar.gz to non-free/a/abyss/abyss_1.2.7-1.debian.tar.gz abyss_1.2.7-1.dsc to non-free/a/abyss/abyss_1.2.7-1.dsc abyss_1.2.7-1_i386.deb to non-free/a/abyss/abyss_1.2.7-1_i386.deb abyss_1.2.7.orig.tar.gz to non-free/a/abyss/abyss_1.2.7.orig.tar.gz -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1qcobk-0001yx...@franck.debian.org
Re: Update of the Integrative Genomics Viewer to version 2.0 ?
Hi Charles, I'm going to be pretty busy for about two weeks. I probably won't have time to look into this until then. If 1.5.65 compiles cleanly and works, there's no harm in uploading that in the mean time. I can take a look into the 2.0 log4j issue two weeks from now. The RollingFileAppender class is at least present in the jar: $ strings /usr/share/java/log4j-1.2-1.2.15.jar |grep /RollingFileAppender.class$ org/apache/log4j/RollingFileAppender.class Cheers, Shaun On 27 June 2011 23:17, Charles Plessy ple...@debian.org wrote: Dear Shaun and everybody, There is a major update of the IGV, which may be interesting to follow. Unfortunately, I have tried to build it from source but could not produce a JAR file that can be executed. I have been reluctant to modify the master branch of the Git repository where we manage the igv package, as there is a version 1.5.65 on the upstream download area, but not in their changelog, which suggests that there may be some maintainance. What shall I do: share work on version 2.0 in our master branch, make a separate branch for the moment, or provide a temporary fork separately ? For the record, the error I get is: log4j:ERROR Could not find value for key log4j.appender.R log4j:ERROR Could not instantiate appender named R. ERROR [2011-06-28 15:16:26,637] [DefaultExceptionHandler.java:42] [main] Unhandled exception java.lang.NoClassDefFoundError: org/apache/log4j/RollingFileAppender at org.broad.igv.ui.Main.initializeLog(Main.java:225) at org.broad.igv.ui.Main.initApplication(Main.java:94) at org.broad.igv.ui.Main.main(Main.java:70) Caused by: java.lang.ClassNotFoundException: org.apache.log4j.RollingFileAppender at java.net.URLClassLoader$1.run(URLClassLoader.java:217) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:205) at java.lang.ClassLoader.loadClass(ClassLoader.java:321) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:294) at java.lang.ClassLoader.loadClass(ClassLoader.java:266) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:334) ... 3 more Have a nice day, -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/banlktik0_a4s8kkp_fs_r6wyh2ehpkb...@mail.gmail.com
Bug#631534: ITP: ABySS -- de novo, parallel, short-read assembler
Package: wnpp Severity: wishlist Package name: abyss Version: 1.2.7 Upstream Author: sjack...@bcgsc.ca URL: http://www.bcgsc.ca/platform/bioinfo/software/abyss License: free for academic use Description: a de novo, parallel, paired-end sequence assembler ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. It may be used to assemble genome or transcriptome sequence data. Parallelization is achieved using MPI, OpenMP and pthread. . To cite your use of ABySS, please reference ABySS: A parallel assembler for short read sequence data. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. Genome Research, 2009-June. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#631534: ITP: ABySS -- de novo, parallel, short-read assembler
Package: wnpp Severity: wishlist Package name: abyss Version: 1.2.7 Upstream Author: sjack...@bcgsc.ca URL: http://www.bcgsc.ca/platform/bioinfo/software/abyss License: free for academic use Description: a de novo, parallel, paired-end sequence assembler ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. It may be used to assemble genome or transcriptome sequence data. Parallelization is achieved using MPI, OpenMP and pthread. . To cite your use of ABySS, please reference ABySS: A parallel assembler for short read sequence data. Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I. Genome Research, 2009-June. -- To UNSUBSCRIBE, email to debian-wnpp-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/BANLkTi=evyn+v+edizpym9exupz4qdo...@mail.gmail.com
bug#8749: mkdir: feature request --reference
Hi Paul, My use case is working in a directory shared amongst a group of users. My umask is 022. I run mkdir -pm775 project/subproject and I'd like both project and project/subproject to be group-writable. Cheers, Shaun On Mon, 2011-05-30 at 22:04 -0700, Paul Eggert wrote: On 05/30/11 10:29, Shaun Jackman wrote: When using mkdir -pm, the specified mode is applied only to the final directory and not the parent directories That behavior is required by POSIX; see http://pubs.opengroup.org/onlinepubs/9699919799/utilities/mkdir.html. Perhaps an argument could be made for a new option, which would have the behavior you'd prefer; it'd be nice to see use cases.
bug#8749: mkdir: feature request --reference
On Tue, 2011-05-31 at 13:06 -0700, Paul Eggert wrote: On 05/31/11 11:12, Shaun Jackman wrote: My use case is working in a directory shared amongst a group of users. My umask is 022. I run mkdir -pm775 project/subproject You're typing stuff like that by hand? I'd expect that sort of thing to be in a script. Either way, you can do this instead: (umask g+w; mkdir -p project/subproject) This is portable and doesn't require any changes to mkdir. Hi Paul, I'm using an alias so that a directory is created with the same permissions as its parent: alias mkdir='mkdir -m $(stat -c%a .)' By hand I'm typing mkdir -p project/subproject Your umask suggestion is good. I hadn't thought of changing the umask in a subshell. Cheers, Shaun
bug#8749: mkdir: feature request --reference
On Tue, 2011-05-31 at 15:49 -0700, Bob Proulx wrote: Shaun Jackman wrote: My use case is working in a directory shared amongst a group of users. My umask is 022. I run If you are working among a group of users then you should set your umask to be 02 instead of 022. That is probably the point where you diverged from common practice and started to have these problems with mkdir. Have you looked at the any of the User Private Group documentation yet? If not then please do so. Good stuff there. mkdir -pm775 project/subproject and I'd like both project and project/subproject to be group-writable. If you set your umask to be 02 then you no longer need to explicitly set the mode bits to ug=rwx,o=rx anymore. Bob Hi Bob, Yes, I have read the documentation on User Private Group. It makes a lot of sense. Currently all the users of my team are in one group, and so my umask is 022. I'll have to talk to my systems group about changing our practice. Cheers, Shaun
bug#8749: mkdir: feature request --reference
On Tue, 2011-05-31 at 15:49 -0700, Bob Proulx wrote: Shaun Jackman wrote: My use case is working in a directory shared amongst a group of users. My umask is 022. I run If you are working among a group of users then you should set your umask to be 02 instead of 022. That is probably the point where you diverged from common practice and started to have these problems with mkdir. Have you looked at the any of the User Private Group documentation yet? If not then please do so. Good stuff there. mkdir -pm775 project/subproject and I'd like both project and project/subproject to be group-writable. If you set your umask to be 02 then you no longer need to explicitly set the mode bits to ug=rwx,o=rx anymore. Bob Hi Bob, It looks like User Private Groups and setgid directories would solve most of my issues except for one. I'd like directories to be group-writable (775) by default and files to group-read-only (644) by default. Andreas suggested using ACL (setfacl -m d:g::rwx), but my file system sadly does not support ACL. Any suggestions? I'm using the following alias for directories that are created interactively: alias mkdir='mkdir -m $(stat -c%a .)' Cheers, Shaun
bug#8749: mkdir: feature request --reference
Hi Bob,
I was using exactly that shell function that you described, but it
doesn't work for
mkdir -p foo/bar
I'm using the alias you gave, which works better. Thanks.
I've noticed one issue, which I feel is a bug in mkdir. When using mkdir
-pm, the specified mode is applied only to the final directory and not
the parent directories:
$ mkdir -pm 775 foo/bar
$ ls -ld foo foo/bar
drwxr-xr-x 3 sjackman assembly 4096 May 30 10:27 foo
drwxrwxr-x 2 sjackman assembly 4096 May 30 10:27 foo/bar
I would expect both foo and foo/bar to have mode 775.
Cheers,
Shaun
On Sat, 2011-05-28 at 18:46 -0700, Bob Proulx wrote:
Shaun Jackman wrote:
My primary use case for this feature is to create a shell alias:
alias mkdir='mkdir --reference=.'
so that in interactive shells, new directories are created with the same
permissions as their parent directory.
If your primary purpose is for an alias then you can do it this way:
alias mkdirchmod='mkdir -m $(stat -c %a .)'
alias mkdirchmod='install -d -m $(stat -c %a .)'
However a shell function might serve you better:
mkdirchmod() { mkdir $@ ; chmod --reference=. $@ ;}
But I think this task is better served by not doing it all and instead
using the technique of User Private Groups.
My goal is to have directories in my personal home directory to have
permission 755 and directories in my shared work space to have
permission 775, so that other members of my group may create new files
in shared directories. Files should have permission 755 so that members
of my group cannot modify files that I've created.
The UPG (User Private Group) technique works very well in this
situation. There is a lot of documentation available on UPG on the
net and so I won't include a specific pointer. Search for it and you
will find a lot of information on it. And different operating systems
deal with configuring it differently and so you would want to look at
documentation for your particular system. But I highly recommend
using the technique.
I generally dislike combining the functionality of several different
commands into one command. In this case combining mkdir and chmod and
I don't see any reason they can't be used individually. Plus mkdir
already allows you to create directories with a specified permission
and this is feature creep into the area of the 'install' command which
also already allows creating directories of specified permissions.
Bob
bug#8749: mkdir: feature request --reference
Hi, mkdir has an option -m to set the permission mode of the directory. I would find it useful for mkdir to have a --reference=FILE option that works identically to chmod. My primary use case for this feature is to create a shell alias: alias mkdir='mkdir --reference=.' so that in interactive shells, new directories are created with the same permissions as their parent directory. My goal is to have directories in my personal home directory to have permission 755 and directories in my shared work space to have permission 775, so that other members of my group may create new files in shared directories. Files should have permission 755 so that members of my group cannot modify files that I've created. Thanks, Shaun
Accepted picard-tools 1.41-1 (source all)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Tue, 22 Mar 2011 10:52:23 -0700 Source: picard-tools Binary: libsam-java picard-tools Architecture: source all Version: 1.41-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: libsam-java - Java library to manipulate SAM and BAM files picard-tools - Command line tools to manipulate SAM and BAM files Closes: 619201 Changes: picard-tools (1.41-1) unstable; urgency=low . * New upstream release. Closes: #619201. * Add five commands to bin/picard-tools and picard-tools.1. Checksums-Sha1: c602497e9ca1f9e15ac0d670050a0d4055287b56 1384 picard-tools_1.41-1.dsc 0a1f13c9fe1144a08d7c92d883b5be3c7c242c47 2978446 picard-tools_1.41.orig.tar.bz2 9aff12e7a3af1f3cf06ad9bdd32e877fae031ed0 6979 picard-tools_1.41-1.debian.tar.gz 2a80aaed944a5bfe3bccacf6f6dbf05f0cdc2f91 193106 libsam-java_1.41-1_all.deb 4c9167b1d99ad4dc6afa2490ba131a635dcbeb82 292812 picard-tools_1.41-1_all.deb Checksums-Sha256: da99d3dca4024e4b200bb150ec0ee6dfbdd79ade657dffe1735c21b1833d2ae1 1384 picard-tools_1.41-1.dsc 6be9d1ee70217094553badddcc64fe5f5c4d007e1282dc069fdbc6eda5db61f9 2978446 picard-tools_1.41.orig.tar.bz2 b30a154ad8e7e7d2803197c80d7a156d39501808d8e1eda9ecba40a391622cbf 6979 picard-tools_1.41-1.debian.tar.gz 8a73f7d69e580bbb7f50082d3380981b35d6f4f3334e4e407c71815fbdfa3806 193106 libsam-java_1.41-1_all.deb eed8cd0d388b3a982d292900c875e9175c93f22520c9364a6570983f6c03c8ac 292812 picard-tools_1.41-1_all.deb Files: 8528f7139756001861f76803aaf8e337 1384 science optional picard-tools_1.41-1.dsc 4eb7772b0ba60ebe88d039c070214f1a 2978446 science optional picard-tools_1.41.orig.tar.bz2 23d9f90ab57a0adb2f49d381a57194ae 6979 science optional picard-tools_1.41-1.debian.tar.gz 648ccf31b18751e5cb3aa1a2b071ca71 193106 java optional libsam-java_1.41-1_all.deb 9cd479eb9aa2a08df26d078b6c60ae00 292812 science optional picard-tools_1.41-1_all.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAk2I4l4ACgkQvFdYF1IwUUrsdgCgn1KHJsdzXYEzLWVdo6tLAuyF z0AAoNB/EYZ/xqtEGC4n3zmbVTimBpog =tscv -END PGP SIGNATURE- Accepted: libsam-java_1.41-1_all.deb to main/p/picard-tools/libsam-java_1.41-1_all.deb picard-tools_1.41-1.debian.tar.gz to main/p/picard-tools/picard-tools_1.41-1.debian.tar.gz picard-tools_1.41-1.dsc to main/p/picard-tools/picard-tools_1.41-1.dsc picard-tools_1.41-1_all.deb to main/p/picard-tools/picard-tools_1.41-1_all.deb picard-tools_1.41.orig.tar.bz2 to main/p/picard-tools/picard-tools_1.41.orig.tar.bz2 -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1q2jqz-0006vb...@franck.debian.org
Accepted gmap 2011-03-11-1 (source i386)
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Format: 1.8 Date: Wed, 23 Mar 2011 10:16:38 -0700 Source: gmap Binary: gmap Architecture: source i386 Version: 2011-03-11-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team debian-med-packag...@lists.alioth.debian.org Changed-By: Shaun Jackman sjack...@debian.org Description: gmap - spliced and SNP-tolerant alignment for mRNA and short reads Changes: gmap (2011-03-11-1) unstable; urgency=low . * New upstream release. Checksums-Sha1: 1e2c4fec8dc3bd980e5b25c79edd571ca65b69c0 1269 gmap_2011-03-11-1.dsc 842f673f6f7b1e8f15c0da835cc450aa0efb47f8 3054718 gmap_2011-03-11.orig.tar.gz d5d96e850318b5c59199f1b847ac8664910c9eae 9905 gmap_2011-03-11-1.debian.tar.gz 9edd3a202ed2dfba75095796f15ff54caf6b5578 4751054 gmap_2011-03-11-1_i386.deb Checksums-Sha256: 0582ba33e0845dc2b96ff8ac9e61634a9b7b9b69f866cbe55ec243f10337adf8 1269 gmap_2011-03-11-1.dsc e8fbafc475b511a38651f8db5f1dd99a470be6543425d13c33f88390ae0d4639 3054718 gmap_2011-03-11.orig.tar.gz 68d0e21839143115bbd6c011d061a59d31a750960462138dcdaff2e422fb80f4 9905 gmap_2011-03-11-1.debian.tar.gz 144420f5fd988ec77aa6ddc787c8779c142e87f357a6708e256574626219aae1 4751054 gmap_2011-03-11-1_i386.deb Files: 0315c3ec242f46284f5a67d2dd0c12fc 1269 non-free/science optional gmap_2011-03-11-1.dsc 8d7a6348018504917e0e1d0dbf32 3054718 non-free/science optional gmap_2011-03-11.orig.tar.gz cda2e359cf57ce496d2641cfa464b103 9905 non-free/science optional gmap_2011-03-11-1.debian.tar.gz 32b7cbb7466463a956c576d261d2eb6a 4751054 non-free/science optional gmap_2011-03-11-1_i386.deb -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAk2KOroACgkQvFdYF1IwUUol8gCaA7cupkXHhE/dNlNJFeUCRrqx QzwAoJ59oDBnuGeemktl9M5OvhEj8+3N =EmkU -END PGP SIGNATURE- Accepted: gmap_2011-03-11-1.debian.tar.gz to non-free/g/gmap/gmap_2011-03-11-1.debian.tar.gz gmap_2011-03-11-1.dsc to non-free/g/gmap/gmap_2011-03-11-1.dsc gmap_2011-03-11-1_i386.deb to non-free/g/gmap/gmap_2011-03-11-1_i386.deb gmap_2011-03-11.orig.tar.gz to non-free/g/gmap/gmap_2011-03-11.orig.tar.gz -- To UNSUBSCRIBE, email to debian-devel-changes-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/e1q2vm2-0006mp...@franck.debian.org
