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
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
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..?
-- Forward
[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'v
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
> > c
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
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 pl
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
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
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
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 g
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
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 see
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 t
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/fa
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
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