Re: Some (minimal?) Java help needed (Was: Bug#670353: ITP: fastqc -- quality control for next generation sequencing data)
Le 11/8/12 8:40 AM, Olivier Sallou a écrit : > Le 11/7/12 3:29 PM, Andreas Tille a écrit : >> Hi, >> >> I stumbled upon this one and did some work on it in >> >>Vcs-Svn: >> http://svn.debian.org/debian-med/trunk/packages/babraham/fastqc/trunk/ >> >> It is close to lintian clean now but there is some CLASSPATH issue >> which is probably very easy for Java experts: >> >> $ fastqc >> Exception in thread "main" java.lang.NoClassDefFoundError: >> uk/ac/babraham/FastQC/FastQCApplication >> Caused by: java.lang.ClassNotFoundException: >> uk.ac.babraham.FastQC.FastQCApplication >> 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) >> Could not find the main class: uk.ac.babraham.FastQC.FastQCApplication. >> Program will exit. >> >> or when trying manually what the wrapper tries to do >> >> $ java -jar /usr/share/fastqc/fastqc.jar >> uk.ac.babraham.FastQC.FastQCApplication >> Skipping 'uk.ac.babraham.FastQC.FastQCApplication' which didn't exist, or >> couldn't be read By the way, should not fastqc.jar be placed in /usr/share/java with version symlink ? > I will have a look but: > It seems that the file with structure > uk/ac/babraham/FastQC/FastQCApplication.class is missing in the jar file > /usr/share/fastqc/fastqc.jar (you can check content with jar -tf > /usr/share/fastqc/fastqc.jar) >> >> My suspicion is that simply specifying the Main-Class in debian/manifest >> is not sufficient. Something might be wrong with the Debian home brewn >> Makefile as quilt patch and ant+built.xml might do a better job to build >> the Jar functionally. Any hint for doing this properly? > Main-Class in manifest gives the default class to call when using java > -jar myjarfile. > If the jar needs other jar files, they need to be specified in Manifest > too or at command line in the classpath parameter. > > Olivier >> Note to obtain the source as easy as possible: Just use the uscan from >> >> >> http://anonscm.debian.org/gitweb/?p=users/tille/devscripts.git;a=blob;f=scripts/uscan.pl >> >> to call >> >>uscan.pl --verbose --force-download --repack-compression xz >> >> which gives you a properly stripped source tarball. >> >> Kind regards and thanks for any help >> >>Andreas. >> >> On Wed, Apr 25, 2012 at 01:08:54AM +0200, Steffen Moeller wrote: >>> Package: wnpp >>> Severity: wishlist >>> Owner: Steffen Moeller >>> >>> * Package name: fastqc >>> * URL : >>> http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ >>> * License : GPL-3 >>> Programming Lang: Java >>> Description : quality control for next generation sequencing data >>> >>> The Debian Med source code repository has some functional (not lintian >>> clean) package in >>> trunk/packages/babraham/fastqc. >>> -- Olivier Sallou IRISA / University of Rennes 1 Campus de Beaulieu, 35000 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) 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/509b66e5.2060...@irisa.fr
Re: Some (minimal?) Java help needed (Was: Bug#670353: ITP: fastqc -- quality control for next generation sequencing data)
Le 11/8/12 8:40 AM, Olivier Sallou a écrit :
> Le 11/7/12 3:29 PM, Andreas Tille a écrit :
>> Hi,
>>
>> I stumbled upon this one and did some work on it in
>>
>>Vcs-Svn:
>> http://svn.debian.org/debian-med/trunk/packages/babraham/fastqc/trunk/
>>
>> It is close to lintian clean now but there is some CLASSPATH issue
>> which is probably very easy for Java experts:
>>
>> $ fastqc
>> Exception in thread "main" java.lang.NoClassDefFoundError:
>> uk/ac/babraham/FastQC/FastQCApplication
>> Caused by: java.lang.ClassNotFoundException:
>> uk.ac.babraham.FastQC.FastQCApplication
>> 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)
>> Could not find the main class: uk.ac.babraham.FastQC.FastQCApplication.
>> Program will exit.
>>
>> or when trying manually what the wrapper tries to do
>>
>> $ java -jar /usr/share/fastqc/fastqc.jar
>> uk.ac.babraham.FastQC.FastQCApplication
>> Skipping 'uk.ac.babraham.FastQC.FastQCApplication' which didn't exist, or
>> couldn't be read
> I will have a look but:
> It seems that the file with structure
> uk/ac/babraham/FastQC/FastQCApplication.class is missing in the jar file
> /usr/share/fastqc/fastqc.jar (you can check content with jar -tf
> /usr/share/fastqc/fastqc.jar)
To get it work, you should fix the /usr/bin/fastq line 183 on exec to get:
exec $java_bin,@java_args,"-jar","/usr/share/fastqc/fastqc.jar", @files;
instead of
exec $java_bin,@java_args, "uk.ac.babraham.FastQC.FastQCApplication",
@files;
and same thing for system call.
>>
>> My suspicion is that simply specifying the Main-Class in debian/manifest
>> is not sufficient. Something might be wrong with the Debian home brewn
>> Makefile as quilt patch and ant+built.xml might do a better job to build
>> the Jar functionally. Any hint for doing this properly?
> Main-Class in manifest gives the default class to call when using java
> -jar myjarfile.
> If the jar needs other jar files, they need to be specified in Manifest
> too or at command line in the classpath parameter.
>
> Olivier
>> Note to obtain the source as easy as possible: Just use the uscan from
>>
>>
>> http://anonscm.debian.org/gitweb/?p=users/tille/devscripts.git;a=blob;f=scripts/uscan.pl
>>
>> to call
>>
>>uscan.pl --verbose --force-download --repack-compression xz
>>
>> which gives you a properly stripped source tarball.
>>
>> Kind regards and thanks for any help
>>
>>Andreas.
>>
>> On Wed, Apr 25, 2012 at 01:08:54AM +0200, Steffen Moeller wrote:
>>> Package: wnpp
>>> Severity: wishlist
>>> Owner: Steffen Moeller
>>>
>>> * Package name: fastqc
>>> * URL :
>>> http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
>>> * License : GPL-3
>>> Programming Lang: Java
>>> Description : quality control for next generation sequencing data
>>>
>>> The Debian Med source code repository has some functional (not lintian
>>> clean) package in
>>> trunk/packages/babraham/fastqc.
>>>
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
Index: fastqc-0.10.1+dfsg.orig/fastqc
===
--- fastqc-0.10.1+dfsg.orig.orig/fastqc 2012-11-08 08:55:51.0 +0100
+++ fastqc-0.10.1+dfsg.orig/fastqc 2012-11-08 09:24:41.0 +0100
@@ -177,10 +177,10 @@
if ($java_bin ne 'java') {
- system $java_bin,@java_args, "uk.ac.babraham.FastQC.FastQCApplication",
@files;
+ system $java_bin,@java_args,"-jar","/usr/share/fastqc/fastqc.jar",
@files;
}
else {
- exec $java_bin,@java_args, "uk.ac.babraham.FastQC.FastQCApplication",
@files;
+ exec $java_bin,@java_args,"-jar","/usr/share/fastqc/fastqc.jar", @files;
}
__DATA__
@@ -273,4 +273,4 @@
Any bugs in fastqc should be reported either to
simon.andr...@babraham.ac.uk
or in www.bioinformatics.babraham.ac.uk/bugzilla/
-
\ No newline at end of file
+
Fwd: Bug#692332: ITP: sga -- A de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representat
I forgot the have the list own this when I sent this ITP out. The packags is at git://git.debian.org/debian-med/sga.git with upstream in master and the package in debian. Feedback is welcome. What is the next step to get bamtools and sga into Debian \ BioLinux \ Ubuntu etc..? -- Forwarded message -- From: Michael Crusoe Date: Sun, Nov 4, 2012 at 7:20 PM Subject: Bug#692332: ITP: sga -- A de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads. To: Debian Bug Tracking System Package: wnpp Severity: wishlist Owner: "Michael R. Crusoe" * Package name: sga Version : 0.9.35 Upstream Author : Jared Simpson * URL : https://github.com/jts/sga * License : GPLv3 Programming Lang: C++ Description : A de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed representation of DNA sequence reads. SGA is a de novo assembler for DNA sequence reads. It is based on Gene Myers' string graph formulation of assembly and uses the FM-index/Burrows-Wheeler transform to efficiently find overlaps between sequence reads. The core algorithms are described in this paper: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/12/i367 -- 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/CAD=wrc+rm0v+m_lzw7j1vfryzm3_ot2vyfca_uw4wv5pxjp...@mail.gmail.com
Re: Bug#692498: ITP: bamtools -- C++ API and toolkit for manipulating BAM (genome alignment) files
[Charles, please make sure you read the end of this mail about samtools!] Hi Michael, On Wed, Nov 07, 2012 at 08:14:38PM -0700, Michael Crusoe wrote: > Pardon me, I forgot to 'reply-all'. No problem (I just mentioned it because I published a "private" mail). > Yeah, I'm new to Git as well. I've made the > git.debian.org/git/debian-med/bamtools.git repository, renamed my > branches, added a pristine-tar based off of the 2.2 release and pushed > up the whole lot. I can confirm that git-buildpackage works. I noticed that you keep what we usually have in branch "upstream" as branch "master" and what we usually call "master" in branch "debian" but this is fine for me and obviosely git-buildpackage has no problem with this. I (as a git beginner) do not see any flaw in this derivation from our policy document so I'd say this is fine (but I need to check later whether my job to gather Vcs metadata can copy with this - I think it can) > >> Okay, I've added the overview of commands: > >> > >> Available bamtools commands: > >> convert Converts between BAM and a number of other formats > >> countPrints number of alignments in BAM file(s) > >> coverage Prints coverage statistics from the input BAM file > >> filter Filters BAM file(s) by user-specified criteria > >> header Prints BAM header information > >> indexGenerates index for BAM file > >> mergeMerge multiple BAM files into single file > >> > > > > Thanks, this is helpful. > > You are welcome. I took the freedom to add further enhancements (git pull). I also tried to silence lintian about the "merge Merge" string in the description but failed. :-( I see no reason why and I'm to lazy to do some deeper inspection - you might like to do this as homework (or we simply drop the override which now adds another warning, or we could s/Merge/Merges/ or whatever you feel apropriate.) > > Hmmm, I wonder whether this is actually a good idea to have versioned > > binary in this way. Is there any good reason to do so? If yes I would > > rather try to do some layout like > > > > /usr/lib/babtools/... > > > > and possibly keep different versions in a reasonable way there which > > could be dealt by setting PATH properly to refer to a certain version. > > You could use a symlink /usr/bin/bamtools to the latest version in > > /usr/lib/bamtools . > > The versioned symlink for the binary is from upstream. My aim here was > to diverge the least amount from what previous users expect. Hmmm, I keep on having a bad feeling with this approach - but if you as the maintainer are considering this as the best for your users I will definitely not insist to follow this gut feeling. However, please use dh_link rather than having a dangling symlink in debian/ - this is ugly enough to change it. > > I have not tested in this case but I'm very positive that debhelper is > > clever enough to do so even without providing these files. > > Testing... Indeed you are correct. I have removed them. The packaging looks good so far. The only thing I would like you to consider is the following: If there are any executable tools inside a library package we usually are creating the following binary package layout: libfoo containing *.so libfoo-dev containing *.a and *.h foo-tools containing executables in /usr/bin The rationale is that from a users point of view it is not obvios that a package strating with lib* contains something to execute and we are not mentioning those packages in our bio task[1] but rather add foo-tools there. The package libfoo-dev is mentioned in the according bio-dev task[2] because it explicitely is targeting at developers. Would you consider to create a bamtools-tools (well, this sounds like a stupid name - perhaps only bam-tools or bamtools-utils - whatever might sound intuitive to you) package? For similarity issues I checked samtools which is formally lacking the libsamtools package - but it also does not contain a *.so dynamic library. Attention to Charles: I just realised that *sam*tools creates a package lib*bam*-dev containing /usr/lib/lib*bam*.a - somehow this sounds wrong to me - please verify whether this is OK. Kind regards Andreas. [1] http://debian-med.alioth.debian.org/tasks/bio [2] http://debian-med.alioth.debian.org/tasks/bio-dev -- 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/20121108085611.ge17...@an3as.eu
Re: Some (minimal?) Java help needed (Was: Bug#670353: ITP: fastqc -- quality control for next generation sequencing data)
On Thu, Nov 08, 2012 at 08:40:06AM +0100, Olivier Sallou wrote: > > or when trying manually what the wrapper tries to do > > > > $ java -jar /usr/share/fastqc/fastqc.jar > > uk.ac.babraham.FastQC.FastQCApplication > > Skipping 'uk.ac.babraham.FastQC.FastQCApplication' which didn't exist, or > > couldn't be read > I will have a look but: > It seems that the file with structure > uk/ac/babraham/FastQC/FastQCApplication.class is missing in the jar file > /usr/share/fastqc/fastqc.jar (you can check content with jar -tf > /usr/share/fastqc/fastqc.jar) Sure, this is what I did in the first place and can confirm $ jar -tf /usr/share/fastqc/fastqc.jar | grep FastQCApplication uk/ac/babraham/FastQC/FastQCApplication$1.class uk/ac/babraham/FastQC/FastQCApplication.class > > My suspicion is that simply specifying the Main-Class in debian/manifest > > is not sufficient. Something might be wrong with the Debian home brewn > > Makefile as quilt patch and ant+built.xml might do a better job to build > > the Jar functionally. Any hint for doing this properly? > Main-Class in manifest gives the default class to call when using java > -jar myjarfile. > If the jar needs other jar files, they need to be specified in Manifest > too or at command line in the classpath parameter. $ cat debian/manifest /usr/share/fastqc/fastqc.jar: Main-Class: uk.ac.babraham.FastQC.FastQCApplication Class-Path: /usr/share/java/jbzip2.jar /usr/share/java/sam.jar ... checking your other mails 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/20121108090047.gf17...@an3as.eu
Re: Bug#692498: ITP: bamtools -- C++ API and toolkit for manipulating BAM (genome alignment) files
On Thu, Nov 8, 2012 at 12:19 AM, Andreas Tille wrote: > On Wed, Nov 07, 2012 at 08:59:27PM -0700, Michael Crusoe wrote: >> On Wed, Nov 7, 2012 at 6:21 AM, Dominique Belhachemi >> wrote: >> > It is also possible to remove the third party code from the source tarball >> > and from debian/copyright. >> >> I've removed it from the master branch and modified the copyright. >> What is the best way to update the source tarball? > > If it is removed from the master branch (you are refering to upstream, > right?) than it might make sense to release a new minor version. I may have mispoke. I removed it from the debian branch. > Otherwise it would make sense to write a debian/get-orig-source script > and call this in the get-orig-source target of debian/rules. There are > a plenty of examples in Debian Med repository - feel free to ask for a > more detailed link. Blergh. That combined with the lack of proper tagging upstream makes for a messy propisition. > 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/20121108071920.gb17...@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/CAD=WrcL4pFTrMYmtd2==awo3eeh7rgacopohockvb_mvbyf...@mail.gmail.com
Re: Some (minimal?) Java help needed (Was: Bug#670353: ITP: fastqc -- quality control for next generation sequencing data)
On Thu, Nov 08, 2012 at 09:01:41AM +0100, Olivier Sallou wrote: > >> $ java -jar /usr/share/fastqc/fastqc.jar > >> uk.ac.babraham.FastQC.FastQCApplication > >> Skipping 'uk.ac.babraham.FastQC.FastQCApplication' which didn't exist, or > >> couldn't be read > By the way, should not fastqc.jar be placed in /usr/share/java with > version symlink ? I confirm that *I* would have done it this way but I did not wanted to change this decision previousely done by Steffen for the moment - specifically not before I got things working. I might change this for the final upload. Thanks for the hint 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/20121108090239.gg17...@an3as.eu
Re: Fwd: Bug#692332: ITP: sga -- A de novo genome assembler based on the concept of string graphs. The major goal of SGA is to be very memory efficient, which is achieved by using a compressed represe
Hi, On Thu, Nov 08, 2012 at 01:19:24AM -0700, Michael Crusoe wrote: > I forgot the have the list own this when I sent this ITP out. Thanks for the foreward (but you are watched anyway and I'm reading all ITPs to debian-devel@l.d.o and all commits in our commits mailing list ;-)) > The packags is at git://git.debian.org/debian-med/sga.git with > upstream in master and the package in debian. > > Feedback is welcome. Just done. > What is the next step to get bamtools and sga into Debian \ BioLinux \ > Ubuntu etc..? I can tell for sure only for Debian: 1. Finalise last issues for bamtools (see my other mail) 2. I (or somebody else of the team) will sponsor the package to the Debian mirrors 3. Wait until ftpmaster accepts the package (might last for two days to two weeks depending on their manpower in the times of freeze - hopefully not longer sometimes this might turn out as a bottleneck but usually these guys are quite fast) 4. Once the package is in unstable it needs to stay there for 10 days without any RC bug and then it migrates to testing - currently we are in freeze time and so it needs to wait until Debian Wheezy is released (hint to everybody: please go and fix remaining RC bugs even if we do not have any such in our team maintained packages) 5. Provided that bemtools will not show any RC bugs it will be part of Debian Wheezy+1 Regarding Ubuntu: It starts after item 3. when Ubuntu drains from unstable (I personally have no idea at which point in time this will happen). Regarding BioLinux: I do not know how Tim is managing this and whether he will wait in any case for an Ubuntu inclusion or whether he might draw the package directly from Debian (unstable ?). Hope this helps 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/20121108091416.gh17...@an3as.eu
Re: Bug#692498: ITP: bamtools -- C++ API and toolkit for manipulating BAM (genome alignment) files
Le Thu, Nov 08, 2012 at 09:56:11AM +0100, Andreas Tille a écrit : > [Charles, please make sure you read the end of this mail about samtools!] > > Attention to Charles: I just realised that *sam*tools creates a package > lib*bam*-dev containing /usr/lib/lib*bam*.a - somehow this sounds wrong > to me - please verify whether this is OK. Hi Andreas, SAM and BAM are two facets of the same format: SAM is tab-delimited text fields, and BAM is indexed binary fields, but the fields are the same, as described in the SAM format specification. http://samtools.sourceforge.net/SAM1.pdf http://samtools.svn.sourceforge.net/viewvc/samtools/trunk/sam-spec/ (By the way, given that the source is available, I was sometimes tempted to package it, but given my current backlog it would be pure procrastination). So it is totally consistent that samtools, which reads and writes SAM and BAM provides a bam library. BamTools is the C++ equivalent of samtools, like Picard is the Java equivalent... The whole naming scheme is not particularly optimal... Cheers, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- 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/20121108093600.ga3...@falafel.plessy.net
Re: Some (minimal?) Java help needed (Was: Bug#670353: ITP: fastqc -- quality control for next generation sequencing data)
On Thu, Nov 08, 2012 at 09:26:27AM +0100, Olivier Sallou wrote: > > > uk/ac/babraham/FastQC/FastQCApplication.class is missing in the jar file > > /usr/share/fastqc/fastqc.jar (you can check content with jar -tf > > /usr/share/fastqc/fastqc.jar) > To get it work, you should fix the /usr/bin/fastq line 183 on exec to get: > > exec $java_bin,@java_args,"-jar","/usr/share/fastqc/fastqc.jar", @files; > > instead of > > exec $java_bin,@java_args, "uk.ac.babraham.FastQC.FastQCApplication", > @files; This sounds somehow obvious and works (even if I wonder why my manual call at command line which exactly did what you suggested was (and is) failing). Thanks for your help 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/20121108100858.gi17...@an3as.eu
Re: Some (minimal?) Java help needed (Was: Bug#670353: ITP: fastqc -- quality control for next generation sequencing data)
Le 11/8/12 11:08 AM, Andreas Tille a écrit :
> On Thu, Nov 08, 2012 at 09:26:27AM +0100, Olivier Sallou wrote:
>>> uk/ac/babraham/FastQC/FastQCApplication.class is missing in the jar file
>>> /usr/share/fastqc/fastqc.jar (you can check content with jar -tf
>>> /usr/share/fastqc/fastqc.jar)
>> To get it work, you should fix the /usr/bin/fastq line 183 on exec to get:
>>
>> exec $java_bin,@java_args,"-jar","/usr/share/fastqc/fastqc.jar", @files;
>>
>> instead of
>>
>> exec $java_bin,@java_args, "uk.ac.babraham.FastQC.FastQCApplication",
>> @files;
>
> This sounds somehow obvious and works (even if I wonder why my manual
> call at command line which exactly did what you suggested was (and is)
> failing).
It seems that the exec call loose the ENV{CLASSPATH} set by the perl
program where dependencies are set. As classpath is correctly set in the
manifest, calling the -jar works perfectly.
If you call on command line: java -cp
/usr/share/fastqc/fastqc.jar:path_tobam.jar:path_to-bzip2.jar
uk.ac.babraham.FastQC.FastQCApplication, it works fine too.
> Thanks for your help
>
>Andreas.
>
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
--
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with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Archive: http://lists.debian.org/509b86bd.3070...@irisa.fr
Re: Some (minimal?) Java help needed (Was: Bug#670353: ITP: fastqc -- quality control for next generation sequencing data)
Hi Olivier,
On Thu, Nov 08, 2012 at 11:17:33AM +0100, Olivier Sallou wrote:
> > This sounds somehow obvious and works (even if I wonder why my manual
> > call at command line which exactly did what you suggested was (and is)
> > failing).
> It seems that the exec call loose the ENV{CLASSPATH} set by the perl
> program where dependencies are set. As classpath is correctly set in the
> manifest, calling the -jar works perfectly.
> If you call on command line: java -cp
> /usr/share/fastqc/fastqc.jar:path_tobam.jar:path_to-bzip2.jar
> uk.ac.babraham.FastQC.FastQCApplication, it works fine too.
I guess this might be an effect of beeing fastqc.jar not in
/usr/share/java where all *.jar files should end up. Whatever, thanks
for enlightening me.
I commited the packaging stuff that creates a fastqc that properly starts
now to SVN. Everybody please give it a test with your sequences.
Unfortunately there seems one remaining issue with the Help system:
If I try the menu item
"Help" -> "Contents..."
I get the following:
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at
uk.ac.babraham.FastQC.FastQCMenuBar.actionPerformed(FastQCMenuBar.java:135)
at
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2012)
at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2335)
at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:404)
at
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:374)
at
javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:829)
at
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:873)
at java.awt.Component.processMouseEvent(Component.java:6389)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3268)
at java.awt.Component.processEvent(Component.java:6154)
at java.awt.Container.processEvent(Container.java:2045)
at java.awt.Component.dispatchEventImpl(Component.java:4750)
at java.awt.Container.dispatchEventImpl(Container.java:2103)
at java.awt.Component.dispatchEvent(Component.java:4576)
at
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4633)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4297)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4227)
at java.awt.Container.dispatchEventImpl(Container.java:2089)
at java.awt.Window.dispatchEventImpl(Window.java:2518)
at java.awt.Component.dispatchEvent(Component.java:4576)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:672)
at java.awt.EventQueue.access$400(EventQueue.java:96)
at java.awt.EventQueue$2.run(EventQueue.java:631)
at java.awt.EventQueue$2.run(EventQueue.java:629)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:105)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:116)
at java.awt.EventQueue$3.run(EventQueue.java:645)
at java.awt.EventQueue$3.run(EventQueue.java:643)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:105)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:642)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:275)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:200)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:185)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:177)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:138)
I tried to find the reason for this pretty useless error log and assumed
that the reason migth possibly be the implicite PATH to the Help dir and
replaced it with an explicite PATH
--- a/uk/ac/babraham/FastQC/FastQCMenuBar.java
+++ b/uk/ac/babraham/FastQC/FastQCMenuBar.java
@@ -132,7 +132,7 @@ public class FastQCMenuBar extends JMenu
}
else if (command.equals("help_contents")) {
try {
- new HelpDialog(application,new
File(URLDecoder.decode(ClassLoader.getSystemResource("Help").getFile(),"UTF-8")));
+ new HelpDialog(application,new
File(URLDecoder.decode(ClassLoader.getSystemResource("/usr/share/fastqc/Help").getFile(),"UTF-8")));
}
catch (UnsupportedEncodingException e1) {
Re: Some (minimal?) Java help needed (Was: Bug#670353: ITP: fastqc -- quality control for next generation sequencing data)
Le 11/8/12 1:13 PM, Andreas Tille a écrit :
> Hi Olivier,
>
> On Thu, Nov 08, 2012 at 11:17:33AM +0100, Olivier Sallou wrote:
>>> This sounds somehow obvious and works (even if I wonder why my manual
>>> call at command line which exactly did what you suggested was (and is)
>>> failing).
>> It seems that the exec call loose the ENV{CLASSPATH} set by the perl
>> program where dependencies are set. As classpath is correctly set in the
>> manifest, calling the -jar works perfectly.
>> If you call on command line: java -cp
>> /usr/share/fastqc/fastqc.jar:path_tobam.jar:path_to-bzip2.jar
>> uk.ac.babraham.FastQC.FastQCApplication, it works fine too.
> I guess this might be an effect of beeing fastqc.jar not in
> /usr/share/java where all *.jar files should end up. Whatever, thanks
> for enlightening me.
>
> I commited the packaging stuff that creates a fastqc that properly starts
> now to SVN. Everybody please give it a test with your sequences.
>
> Unfortunately there seems one remaining issue with the Help system:
> If I try the menu item
>
>"Help" -> "Contents..."
>
> I get the following:
>
> Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
> at
> uk.ac.babraham.FastQC.FastQCMenuBar.actionPerformed(FastQCMenuBar.java:135)
> at
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2012)
> at
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2335)
> at
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:404)
> at
> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
> at javax.swing.AbstractButton.doClick(AbstractButton.java:374)
> at
> javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:829)
> at
> javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:873)
> at java.awt.Component.processMouseEvent(Component.java:6389)
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3268)
> at java.awt.Component.processEvent(Component.java:6154)
> at java.awt.Container.processEvent(Container.java:2045)
> at java.awt.Component.dispatchEventImpl(Component.java:4750)
> at java.awt.Container.dispatchEventImpl(Container.java:2103)
> at java.awt.Component.dispatchEvent(Component.java:4576)
> at
> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4633)
> at
> java.awt.LightweightDispatcher.processMouseEvent(Container.java:4297)
> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4227)
> at java.awt.Container.dispatchEventImpl(Container.java:2089)
> at java.awt.Window.dispatchEventImpl(Window.java:2518)
> at java.awt.Component.dispatchEvent(Component.java:4576)
> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:672)
> at java.awt.EventQueue.access$400(EventQueue.java:96)
> at java.awt.EventQueue$2.run(EventQueue.java:631)
> at java.awt.EventQueue$2.run(EventQueue.java:629)
> at java.security.AccessController.doPrivileged(Native Method)
> at
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:105)
> at
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:116)
> at java.awt.EventQueue$3.run(EventQueue.java:645)
> at java.awt.EventQueue$3.run(EventQueue.java:643)
> at java.security.AccessController.doPrivileged(Native Method)
> at
> java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:105)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:642)
> at
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:275)
> at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:200)
> at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
> at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:185)
> at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:177)
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:138)
>
> I tried to find the reason for this pretty useless error log and assumed
> that the reason migth possibly be the implicite PATH to the Help dir and
> replaced it with an explicite PATH
>
> --- a/uk/ac/babraham/FastQC/FastQCMenuBar.java
> +++ b/uk/ac/babraham/FastQC/FastQCMenuBar.java
> @@ -132,7 +132,7 @@ public class FastQCMenuBar extends JMenu
> }
>
> else if (command.equals("help_contents")) {
>
> try {
>
> - new HelpDialog(application,new
> File(URLDecoder.decode(ClassLoader.getSystemResource("Help").getFile(),"UTF-8")));
>
> + new HelpDialog(application,new
>
Re: Bug#692498: ITP: bamtools -- C++ API and toolkit for manipulating BAM (genome alignment) files
On Thu, Nov 08, 2012 at 01:45:39AM -0700, Michael Crusoe wrote: > On Thu, Nov 8, 2012 at 12:19 AM, Andreas Tille wrote: > > On Wed, Nov 07, 2012 at 08:59:27PM -0700, Michael Crusoe wrote: > >> On Wed, Nov 7, 2012 at 6:21 AM, Dominique Belhachemi > >> wrote: > >> > It is also possible to remove the third party code from the source > >> > tarball > >> > and from debian/copyright. > >> > >> I've removed it from the master branch and modified the copyright. > >> What is the best way to update the source tarball? > > > > If it is removed from the master branch (you are refering to upstream, > > right?) than it might make sense to release a new minor version. > > I may have mispoke. I removed it from the debian branch. OK. Unfortunately it remains in the pristine-tar and when using git-buildpackage it creates a tarball including the third_party dir. If I simply use the get-orig-source target and drop the result in ../tarballs I can trick git-buildpackage with this new tarball. Works somehow but hmmm, its a bit hackish. We could end up with a situation where somebody else would like to rebuild the package, will trust what is in pristine-tar and ends up with an upstream tarball with different MD5 sum which will be rejected at the Debian mirror. So fixing pristine-tar would make really sense - unfortunately I have no idea how to do this properly. I tried $ git import-orig --pristine-tar ../tarballs/bamtools_2.2.orig.tar.gz What is the upstream version? [2.2] gbp:info: Importing '../tarballs/bamtools_2.2.orig.tar.gz' to branch 'master'... gbp:info: Source package is bamtools gbp:info: Upstream version is 2.2 pristine-tar: committed bamtools_2.2.orig.tar.gz.delta to branch pristine-tar fatal: tag 'upstream/2.2' already exists gbp:error: Couldn't run git tag: git returned 128 gbp:error: Import of ../tarballs/bamtools_2.2.orig.tar.gz failed so this does not do the trick. :-( > > Otherwise it would make sense to write a debian/get-orig-source script > > and call this in the get-orig-source target of debian/rules. There are > > a plenty of examples in Debian Med repository - feel free to ask for a > > more detailed link. > > Blergh. That combined with the lack of proper tagging upstream makes > for a messy propisition. Yep. A fair amount of Debian package maintenance is teaching upstream. As I said in the beginning: It would be *really* helpful if upstream would consider providing release tarballs at some http location. We could write a debian/watch file and would have way less burden to get the source properly. BTW, please do `git pull` for some changes in the get-orig-source target. Anything about replacing the dangling symlink by a dh_link call by using a libbamtools2.2.0.links file? 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/20121108124148.gk17...@an3as.eu
FastQC read for testing (Was: Some (minimal?) Java help needed)
On Thu, Nov 08, 2012 at 01:22:52PM +0100, Olivier Sallou wrote:
> Looking at the code, I would expect to get something like:
>
>
> new HelpDialog(application,new
> File(URLDecoder.decode("/usr/share/fastqc/Help","UTF-8")));
> or
> new HelpDialog(application,new File("/usr/share/fastqc/Help");
>
> Olivier
I can confirm that this works (see SVN).
Any volunteer to test the lintian clean package with some real data
before I upload? Steffen?
Kind regards
Andreas.
--
http://fam-tille.de
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Archive: http://lists.debian.org/20121108130059.gl17...@an3as.eu
Re: Bug#692498: ITP: bamtools -- C++ API and toolkit for manipulating BAM (genome alignment) files
Le Thu, Nov 08, 2012 at 01:41:48PM +0100, Andreas Tille a écrit : > > Yep. A fair amount of Debian package maintenance is teaching upstream. > As I said in the beginning: It would be *really* helpful if upstream > would consider providing release tarballs at some http location. We > could write a debian/watch file and would have way less burden to get > the source properly. Hi all, If the BamTools developers would push git tags to GitHub, then it would make tarballs for free. See for instance BEDTools: https://github.com/arq5x/bedtools/tags Cheers, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan -- 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/20121108234516.gd22...@falafel.plessy.net
