Re: GATK

Hi Andreas, Le 14/07/2023 à 08:14, Andreas Tille a écrit : Hi Pierre, [...] Right now I am preparing the move of my family some hundreds of kilometers away, I expect to get more time to look at it closer afterwards. Sure, Real life should have preference over volunteer work. Is the

Re: GATK

Hi Pierre, Am Thu, Jul 13, 2023 at 10:23:10PM +0200 schrieb Pierre Gruet: > Yeah, GATK is one of my main goals, with Nextflow. If I remember correctly, > scala was a blocker but there might be a way to deal with it... Thanks a lot! > Right now I am preparing the move of my family some

Re: GATK

Hi Andreas, Le 12/07/2023 à 15:01, Andreas Tille a écrit : Hi Pierre, I was wondering whether we might be able to package GATK for the next release. I've just fixed the watch file in Git. It would be great if you could have a look once you might find some spare cycles. Yeah, GATK is one

GATK

Hi Pierre, I was wondering whether we might be able to package GATK for the next release. I've just fixed the watch file in Git. It would be great if you could have a look once you might find some spare cycles. Kind regards Andreas. -- http://fam-tille.de

Bug#1014344: marked as done (ITP: gatk-bwamem -- interface to call Heng Li's bwa mem aligner from Java code)

Your message dated Fri, 22 Jul 2022 19:10:10 + with message-id and subject line Bug#1014344: fixed in gatk-bwamem 1.0.4+dfsg2-1 has caused the Debian Bug report #1014344, regarding ITP: gatk-bwamem -- interface to call Heng Li's bwa mem aligner from Java code to be marked as done

Bug#1014344: ITP: gatk-bwamem -- interface to call Heng Li's bwa mem aligner from Java code

Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: gatk-bwamem Version : 1.0.4 Upstream Author : Broad Institute * URL : https://github.com/broadinstitute/gatk-bwamem-jni

Bug#1008128: marked as done (ITP: gatk-fermilite -- interface to call Heng Li's fermi-lite assembler from Java code)

Your message dated Tue, 05 Apr 2022 18:00:13 + with message-id and subject line Bug#1008128: fixed in gatk-fermilite 1.2.1+dfsg-1 has caused the Debian Bug report #1008128, regarding ITP: gatk-fermilite -- interface to call Heng Li's fermi-lite assembler from Java code to be marked as done

Bug#1008128: ITP: gatk-fermilite -- interface to call Heng Li's fermi-lite assembler from Java code

Package: wnpp Severity: wishlist Owner: Debian-med team X-Debbugs-Cc: debian-de...@lists.debian.org, debian-med@lists.debian.org * Package name: gatk-fermilite Version : 1.2.1 Upstream Author : Broad Institute * URL : https://github.com/broadinstitute/gatk-fermilite

Re: Advice needed: building new gatk-bwamem-jni against another version of bwa

Hi Andrius, Thanks for looking at my issue. Le 14/03/2022 à 06:03, Andrius Merkys a écrit : Hi Pierre, On 2022-03-13 16:35, Pierre Gruet wrote: My proposal would be to design a multiple upstream tarball for gatk-bwamem-jni: original one + the sources at the tip of the Apache2 branch of bwa

Re: Advice needed: building new gatk-bwamem-jni against another version of bwa

Hi Pierre, On 2022-03-13 16:35, Pierre Gruet wrote: > My proposal would be to design a multiple upstream tarball for > gatk-bwamem-jni: original one + the sources at the tip of the Apache2 > branch of bwa. It would build a libbwa.a lib which would not be > installed in /usr/lib, but

Re: Advice needed: building new gatk-bwamem-jni against another version of bwa

Hi Nilesh, Thanks for the quick answer. Your advice is much appreciated, as always. Le 13/03/2022 à 15:46, Nilesh Patra a écrit : On 3/13/22 8:05 PM, Pierre Gruet wrote: What should I do? My proposal would be to design a multiple upstream tarball for gatk-bwamem-jni: original one

Re: Advice needed: building new gatk-bwamem-jni against another version of bwa

On 3/13/22 8:05 PM, Pierre Gruet wrote: What should I do? My proposal would be to design a multiple upstream tarball for gatk-bwamem-jni: original one + the sources at the tip of the Apache2 branch of bwa.> It would build a libbwa.a lib which would not be installed in /usr/

Advice needed: building new gatk-bwamem-jni against another version of bwa

Hello everyone, I need your advice on a packaging issue I am meeting right now. I am in the course of packaging gatk-bwamem-jni [0], providing a native interface which allows one to use bwa (Debian packaged [1]) from Java code. Fine. But the upstream of gatk-bwamem-jni relies on a version

About gatk -- git-lfs and dependencies to be packaged

Hi everyone, Recently there has been quite a lot of movement around the packaging of gatk: - I listed the dependencies to be packaged in our common spreadsheet, in the Java sheet, on lines 61 to 78. I think some of them should reveal optional, but I also see at some point we will be blocked

Re: /usr/bin/picard Re: bcbio will need another while - needs gatk

Hi Steffen, On Sat, Nov 14, 2020 at 10:44:36PM +0100, Steffen Möller wrote: > > https://www.bioconductor.org/packages/release/bioc/html/TitanCNA.html Uploaded to new. > https://bioconductor.org/packages/release/bioc/html/PureCN.html Pushed to Git but 3 remaining errors in autopkgtest. > How

Re: Progress of Snpeff packaging (Was: Re: /usr/bin/picard Re: bcbio will need another while - needs gatk)

Hi Pierre, thanks a lot for your continuous work on snpeff! On Thu, Nov 19, 2020 at 08:34:10PM +0100, Pierre Gruet wrote: > > It's good we talk about it. There were 4 identified missing packages to > be able to complete the packaging of Snpeff; 3 of them are now in > Debian, only akka-actor

Progress of Snpeff packaging (Was: Re: /usr/bin/picard Re: bcbio will need another while - needs gatk)

Hi, Le 15/11/2020 à 18:16, Andreas Tille a écrit : > >> >> This may be worth a sidenote - bcbio to me is something metaphorical. We >> have it in the distribution already. And now we work to get all the >> runtime-dependencies in to make it functional. And snpEff is pretty high >> up (it

Re: /usr/bin/picard Re: bcbio will need another while - needs gatk

Hi Steffen, On Sun, Nov 15, 2020 at 02:39:03PM +0100, Steffen Möller wrote: > >> I just checked what my installation has in this directory ... and it > >> seems like I spotted a typo (or a creative fix of a typo elsewhere) > > ? > tranlate misses the "s" Fixed in new upload. BTW, it would be

Re: /usr/bin/picard Re: bcbio will need another while - needs gatk

oft[1] and lots of other packages. Simply >>> provide this for picard-tools and make sure gatk users set the PATH >>> accordingly. >> Ah - that is good. Seems like I should read our policy document again. > Not sure whether it is mentioned in policy. I introduced t

Re: [RFS] gsort and dependencies (Was: /usr/bin/picard Re: bcbio will need another while - needs gatk)

Hi Nilesh, Impressive as usual. On 15.11.20 12:17, Nilesh Patra wrote: > Hi, > > I packaged gsort and the rest of the dependency chain as needed by > bcbio. Everything seems to build+pass its autopkgtests. > > The dependency chain is as follows: > > 1. golang-github-alexflint-go-scalar [1] > 2.

[RFS] gsort and dependencies (Was: /usr/bin/picard Re: bcbio will need another while - needs gatk)

Hi, I packaged gsort and the rest of the dependency chain as needed by bcbio. Everything seems to build+pass its autopkgtests. The dependency chain is as follows: 1. golang-github-alexflint-go-scalar [1] 2. golang-github-alexflint-go-arg [2](depends on [1]) 3. ggd-utils [3] (depends on

Re: /usr/bin/picard Re: bcbio will need another while - needs gatk

On Sun, 15 Nov 2020 at 02:34, Andreas Tille wrote: > On Sun, Nov 15, 2020 at 01:21:05AM +0530, Nilesh Patra wrote: > > > > I did have a look earlier today. > > gsort has dependency on unpackaged packages - " > > https://github.com/alexflint/go-arg; and " > >

Re: /usr/bin/picard Re: bcbio will need another while - needs gatk

On 14.11.20 20:18, Steffen Möller wrote: > I presume you would be happy for me to put there a link from cnvkit.py > (like bcbio expects it) to /usr/bin/cnvkit, right? Update: I patched bcbio to find it. While looking at the source tree of the cnvkit wrapper of bcbio I found that it references

Re: /usr/bin/picard Re: bcbio will need another while - needs gatk

Hi Nilesh, On 14.11.20 20:51, Nilesh Patra wrote: > > On Sun, 15 Nov 2020 at 00:49, Steffen Möller > wrote: > > >> Should we have someone among us for who packaging go-based software > >> feels like easy then the newly surfaced >

Re: /usr/bin/picard Re: bcbio will need another while - needs gatk

On Sun, Nov 15, 2020 at 01:21:05AM +0530, Nilesh Patra wrote: > > I did have a look earlier today. > gsort has dependency on unpackaged packages - " > https://github.com/alexflint/go-arg; and " > https://github.com/gogetdata/ggd-utils; > > and "https://github.com/alexflint/go-arg; has dep on " >

Re: /usr/bin/picard Re: bcbio will need another while - needs gatk

Hi Steffen, On Sat, Nov 14, 2020 at 08:18:48PM +0100, Steffen Möller wrote: > > We have the workaround > > > > /usr/lib/debian-med/bin/ > > > > see for instance in eigensoft[1] and lots of other packages. Simply > > provide this for picard-tools a

Re: /usr/bin/picard Re: bcbio will need another while - needs gatk

Hi Andreas and Steffen On Sun, 15 Nov 2020 at 00:49, Steffen Möller wrote: > >> Should we have someone among us for who packaging go-based software > >> feels like easy then the newly surfaced https://github.com/brentp/gsort > >> would be nice. > > Nilesh did so several times. > Wow! @Nilesh,

Re: /usr/bin/picard Re: bcbio will need another while - needs gatk

Hi Andreas, On 14.11.20 09:43, Andreas Tille wrote: > On Fri, Nov 13, 2020 at 10:25:39PM +0100, Steffen Möller wrote: >> I installed a binary distribution of gatk and then ran a bit into >> trouble over >> >> $ apt-file search /usr/bin/picard >> picard: /usr/bin

Re: /usr/bin/picard Re: bcbio will need another while - needs gatk

Hi Steffen, On Fri, Nov 13, 2020 at 10:25:39PM +0100, Steffen Möller wrote: > I installed a binary distribution of gatk and then ran a bit into > trouble over > > $ apt-file search /usr/bin/picard > picard: /usr/bin/picard > picard-tools: /usr/bin/picard-tools &g

/usr/bin/picard Re: bcbio will need another while - needs gatk

Hello, I installed a binary distribution of gatk and then ran a bit into trouble over $ apt-file search /usr/bin/picard picard: /usr/bin/picard picard-tools: /usr/bin/picard-tools I tend to think that this exposes a weakness of Debian - it misses namespaces. Others may say that it is a strength

bcbio will need another while - needs gatk

[2020-11-12T20:56Z] /usr/bin/bash: line 1: gatk: command not found There are also other issues, like use using a newer version of STAR (rna-star) and the file testing against is not prepared for that. Kind of neat: The hts-nim-tools should have an executable with hyphens, not underscores. Conda

gatk: Any hint for Java (Maven) packaging

Hi, I just commited Vcs-Git: git://anonscm.debian.org/debian-med/gatk.git I had no real luck with mh_make which only created debian/maven.* files but no d/contol and d/rules file due to some error in the last step. I also noticed the following output from mh_make process: In pom.xml: This