Bug#848758: [Debian-med-packaging] Bug#848758: python-skbio: FTBFS: Test failures
Hi all,
On 22:19 19/12, Lucas Nussbaum wrote:
> Source: python-skbio
> Version: 0.5.1-1
> Severity: serious
> Tags: stretch sid
> User: debian...@lists.debian.org
> Usertags: qa-ftbfs-20161219 qa-ftbfs
> Justification: FTBFS on amd64
>
> Hi,
>
> During a rebuild of all packages in sid, your package failed to build on
> amd64.
>
> Relevant part (hopefully):
> > multiple_comparisons_correction=None)
> > File
> > "/<>/.pybuild/pythonX.Y_3.5/build/skbio/stats/composition.py",
> > line 971, in ancom
> > _logratio_mat = _log_compare(mat.values, cats.values, significance_test)
> > File
> > "/<>/.pybuild/pythonX.Y_3.5/build/skbio/stats/composition.py",
> > line 1084, in _log_compare
> > arr=ratio)
> > File "/usr/lib/python3/dist-packages/numpy/lib/shape_base.py", line 133,
> > in apply_along_axis
> > if res.shape == ():
> > AttributeError: 'F_onewayResult' object has no attribute 'shape'
> >
> > --
> > Ran 2238 tests in 42.139s
> >
> > FAILED (SKIP=30, errors=15)
> > E: pybuild pybuild:276: test: plugin distutils failed with: exit code=1: cd
> > /<>/.pybuild/pythonX.Y_3.5/build; python3.5 -m nose
> > dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.5 returned
> > exit code 13
> > debian/rules:22: recipe for target 'override_dh_auto_test' failed
Upstream has now fixed this issue, and I've cherry-picked the fix into the
package as a patch. I've pushed to git.d.o, so an (urgent) upload would be much
appreciated.
Merry Christmas all!
Cheers
K
---
Kevin Murray
Bug#845982: cwltool accesses internet -- missing dependency
Hi Ghis, On 11:39 06/12, Ghislain Vaillant wrote: > On Sun, 4 Dec 2016 11:08:35 +1100 Kevin Murray <kdmf...@gmail.com> wrote: > I can do it if time is limited for you. I am dealing with a different chain of > package dependencies which would require keepalive being packaged too. That would be great, the pre-Christmas rush is well and truly upon me at work, so time is very limited at the moment. Thanks heaps, Kevin --- Kevin Murray
Bug#846958: src:iqtree: New version available
Hi Andreas, On 17:44 04/12, Andreas Tille wrote: > Kevin Murray added a Closes statement to its latest commits to iqtree. > This is the according bug report. :-) Kevin, please tell me if you > consider iqtree ready for Upload. I was just waiting on the BTS to give me a bug number. Should be good to go now thanks Andreas! Cheers, K --- Kevin Murray
Bug#845982: cwltool accesses internet -- missing dependency
Hi, I had a look at the build of cwltool, and it appears it depends upon the `keepalive` python package. I will file an RFS bug for this (and prepare a package as time permits). Cheers, K --- Kevin Murray
Bug#846664: [Debian-med-packaging] Bug#846664: Bug#846664: src:adapterremoval: New version available
Hi all, On 07:52 03/12, Andreas Tille wrote: > Hi, > > there is a new upstream version of adapterremoval. I have deactivated > the attempt to create an adapterremoval-benchmark package for the moment > so feel free to upgrade to the latest upstream version if you like to. I've now prepared the package of the latest upstream release, so a review & upload would be required. Thanks in advance! Cheers, K --- Kevin Murray
Bug#846664: [Debian-med-packaging] Bug#846664: src:adapterremoval: New version available
As mentioned, I'll do this (tomorrow). Cheers, K On 07:52 03/12, Andreas Tille wrote: > Package: src:adapterremoval > Severity: normal > > Hi, > > there is a new upstream version of adapterremoval. I have deactivated > the attempt to create an adapterremoval-benchmark package for the moment > so feel free to upgrade to the latest upstream version if you like to. > > Kind regards > > Andreas. > > -- System Information: > Debian Release: 8.6 > APT prefers stable-updates > APT policy: (500, 'stable-updates'), (500, 'stable') > Architecture: amd64 (x86_64) > > Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core) > Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8) > Shell: /bin/sh linked to /bin/dash > Init: systemd (via /run/systemd/system) > > ___ > Debian-med-packaging mailing list > debian-med-packag...@lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging --- Kevin Murray
Bug#845737: New release
Hi Santiago, Thanks for the bug report. I've reported this issue to upstream[1]. In the mean time, I've recently packaged the newest upstream release. Could you please re-run your tests (or advise me how to) for this new version. FWIW, I have experienced issues related to POSIX semaphores when building this package in pbuider chroots, related to a missing /dev/shm. I have never experienced the issues you report though. Cheers, K [1]: https://bitbucket.org/snakemake/snakemake/issues/426/random-test-hangs-during-debian-package --- Kevin Murray
Bug#841560: [Debian-med-packaging] Bug#841560: Could anybody please check the issue in python-skbio
Hi all, AFAICT I think I should have fixed the issues in skbio. I've filed an ROM bug, and updated to latest upstream. Could I please get an upload and see if the test failure goes away? Cheers, Kevin --- Kevin Murray
Bug#841560: [Debian-med-packaging] Bug#841560: Bug#841560: Could anybody please check the issue in python-skbio
Hi Andreas, On 19:15 15/11, Kevin Murray wrote: > I will also (but haven't yet) see if I can get it to build against libssw. Well that turned out to be far easier than I expected. I've pushed a patch that uses libssw from debian. So let's see if this fixes the build. And we also need to remove the old binary pkgs from the archive, I think (or whatever the reason is for the package being stuck in sid). Cheers, K --- Kevin Murray
Bug#841560: [Debian-med-packaging] Bug#841560: Could anybody please check the issue in python-skbio
Hi Andreas, On 08:49 15/11, Andreas Tille wrote: > could anybody check the issue in the skbio test suite? I've packaged the latest upstream, and uploaded. Let's see if this fixes the build. I will also (but haven't yet) see if I can get it to build against libssw. There are also old binary packages preventing a testing transition, which I'm not sure how to deal with. Cheers, K --- Kevin Murray
Bug#836574: [Debian-med-packaging] Bug#836574: What about the license change, PATENTS file, etc. ?
I honestly have no idea, but from the discussion that has ensued in that issue at Github, it seems this is a blanket statement that Facebook puts in all their free software projects. IANAL, but nothing there seems specific to Zstd. Cheers, Kevin On 21:54 04/09, Aleks-Daniel Jakimenko-Aleksejev wrote: > See this: https://github.com/facebook/zstd/issues/335 > > Is everything alright? > ___ > Debian-med-packaging mailing list > debian-med-packag...@lists.alioth.debian.org > http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging --- Kevin Murray
Bug#836574: [Debian-med-packaging] Bug#836574: libzstd: new upstream version available
Hi Daniel, I've prepared the update. I'll push as soon as git.debian.org returns to the internet. Cheers, K --- Kevin Murray
Bug#816153: python-falcon: Documentation is not packaged
Package: python-falcon
Version: 0.3.0-5
Severity: normal
Dear Maintainer,
I found that python-falcon does not build or package its documentation.
So I attach patches to build and package the sphinx documentation in a
new python-falcon-doc package.
Additionally, I have added autopkgtests that run the test suite, and fix
a lintian warning about a missing manpage.
Cheers,
Kevin
P.S. Apologies if this is submitted twice, I've been having issues with
reportbug.
-- System Information:
Debian Release: stretch/sid
APT prefers testing
APT policy: (900, 'testing'), (500, 'testing-updates'), (500,
'stable-updates'), (400, 'unstable'), (300, 'stable')
Architecture: amd64 (x86_64)
Kernel: Linux 4.3.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
Versions of packages python-falcon depends on:
ii libc6 2.21-9
ii python2.7.11-1
ii python-mimeparse 0.1.4-1
ii python-six1.10.0-2
pn python:any
python-falcon recommends no packages.
python-falcon suggests no packages.
-- no debconf information
---
Kevin Murray
0xA4B4EE6A
>From 990ed5fd996290c31f2a06491d8d5966ca10e31d Mon Sep 17 00:00:00 2001
From: Kevin Murray <s...@kdmurray.id.au>
Date: Mon, 22 Feb 2016 07:48:39 +1100
Subject: [PATCH 1/5] Build sphinx docs; package into python-falcon-do
---
debian/control | 36
debian/patches/series | 1 +
debian/patches/sphinx-13+-napoleon | 16
debian/python-falcon-doc.doc-base | 9 +
debian/python-falcon-doc.install | 1 +
debian/rules | 6 +-
6 files changed, 68 insertions(+), 1 deletion(-)
create mode 100644 debian/patches/sphinx-13+-napoleon
create mode 100644 debian/python-falcon-doc.doc-base
create mode 100644 debian/python-falcon-doc.install
diff --git a/debian/control b/debian/control
index a39a082..e7480d0 100644
--- a/debian/control
+++ b/debian/control
@@ -29,6 +29,8 @@ Build-Depends: cython,
python3-six,
python3-testtools,
python3-yaml,
+ python-sphinx,
+ python3-sphinx,
Standards-Version: 3.9.6
Vcs-Browser: http://anonscm.debian.org/gitweb/?p=openstack/python-falcon.git
Vcs-Git: git://anonscm.debian.org/openstack/python-falcon.git
@@ -42,6 +44,7 @@ Depends: python-mimeparse,
${python:Depends},
${shlibs:Depends},
Recommends: ${python:Recommends},
+Suggests: python-falcon-doc ( = ${source:Version})
Description: supersonic micro-framework for building cloud APIs - Python 2.x
Falcon is a high-performance Python framework for building cloud APIs. It
encourages the REST architectural style, and tries to do as little as possible
@@ -74,6 +77,7 @@ Depends: python3-mimeparse,
${python3:Depends},
${shlibs:Depends},
Recommends: ${python3:Recommends},
+Suggests: python-falcon-doc ( = ${source:Version})
Description: supersonic micro-framework for building cloud APIs - Python 3.x
Falcon is a high-performance Python framework for building cloud APIs. It
encourages the REST architectural style, and tries to do as little as possible
@@ -97,3 +101,35 @@ Description: supersonic micro-framework for building cloud APIs - Python 3.x
* Python 2.6, Python 2.7, PyPy and Python 3.3 support
.
This package provides the Python 3.x module.
+
+Package: python-falcon-doc
+Architecture: all
+Section: doc
+Depends: ${misc:Depends},
+ ${shlibs:Depends},
+ ${sphinxdoc:Depends},
+Recommends: python3-falcon ( = ${source:Version}) | python-falcon ( = ${source:Version})
+Description: supersonic micro-framework for building cloud APIs - Documentation
+ Falcon is a high-performance Python framework for building cloud APIs. It
+ encourages the REST architectural style, and tries to do as little as possible
+ while remaining highly effective.
+ .
+ Unlike other Python web frameworks, Falcon won't bottleneck your API's
+ performance under highly concurrent workloads. Many frameworks max out at
+ serving simple "hello world" requests at a few thousand req/sec, while Falcon
+ can easily serve many more on the same hardware.
+ .
+ Falcon isn't very opinionated. In other words, the framework leaves a lot of
+ decisions and implementation details to you.
+ .
+ Features:
+ * Intuitive routing via URI templates and resource classes
+ * Easy access to headers and bodies through request and response classes
+ * Idiomatic HTTP error responses via a handy exception base class
+ * DRY request processing using global, resource, and method hooks
+ * Snappy unit testing through WSGI helpers and mocks
+ * 20% speed boost when Cython is available
+ * Python 2.6, Python 2.7, PyPy and Python 3.3 support
+ .
+ This package provides the sphinx API documentation and user guide.
+
diff --git a/debian/patc
Bug#815631: sphinx: Use alternatives to provide scripts under /usr/bin
Hi Dmitry,
Thanks for your advice.
On 10:19 23/02, Dmitry Shachnev wrote:
> Hi Kevin,
>
> On Tue, Feb 23, 2016 at 02:34:11PM +1100, Kevin Murray wrote:
> > I have recently needed to use a python3-only sphinx build process on a
> > system with both python-sphinx & python3-sphinx co-installed. IMHO
> > co-installation could be a little cleaner and easier if sphinx:
> >
> > - Used update-alternatives to provide /usr/bin/sphinx-* in a
> > configurable way. (e.g similar to how docutils handles this problem). This
> > could use the current script installation path under
> > /usr/share/sphinx/scripts/python*/
>
> Let me quote Jakub Wilk, who wrote the current implementation:
>
> The alternatives mechanism is only suitable if both commands are compatible,
> i.e. their behavior doesn't vary with Python version. This is the case for
> rst2html and friends, but no so much for sphinx-build. The problem is that
> sphinx-build can import 3rd-party Python code, which is not necessarily
> compatible with both Python 2 and 3.
>
Ah, that's something I didn't consider. Good point.
> > - Or, installed binaries under /usr/bin with the suffix '3', i.e. install
> > /usr/bin/sphinx-build3. (modelled after pip/pip3 & nosetests/nosetests3
> > and other similar examples)
>
> The name of sphinx-build command is hardcoded in too many places (i.e. the
> Makefiles generated by Sphinx use it). Also, I don't much like the foo/foo3
> naming because there is a better way: pythonX[.Y] -m sphinx allows one to
> call sphinx-build with *any* Python version (not necessarily the default one).
>
Ah yes, that's true about hardcoding. This is actually why I need this:
hardcoded occurrences of sphinx-build in makefiles that aren't in python
projects but use (and only work with) python3 packages. And thanks for the tip
about python -m sphinx, I hadn't considered that. Though for the current use
case still means patching a makefile, in which case I'll just include the full
path to the installed script under /usr/share/sphinx.
> > - Or, a combination of both these, where python-sphinx and
> > python3-sphinx install /usr/bin/sphinx-*{2,3} respectively, and
> > update-alternatives is used to provide /usr/bin/sphinx-* without
> > prefix.
>
> See above.
>
> > P.S., I know one can always do
> > /usr/share/sphinx/scripts/python3/sphinx-build
> > as a workaround.
>
> What is exactly your problem? Does Python 2 sphinx not work with your code?
> Can you use python3 -m sphinx there? Or maybe use setuptools' build_sphinx
> command?
The problem was to use python3-sphinx from a Makefile (not an auto-generated
sphinx-quickstart one) without patching the makefile. Given your descriptions
above, I think that there are better ways of solving this problem than what I
proposed.
*However*, there is a supplementary issue: AFAICT, which package provides the
/usr/bin/sphinx-* scripts depends on the order of installation. To me this
sounds a little off, but I'm not sure. What is your opinion of this?
Cheers,
K
---
Kevin Murray
0xA4B4EE6A
signature.asc
Description: PGP signature
Bug#815631: sphinx: Use alternatives to provide scripts under /usr/bin
Source: sphinx
Severity: normal
Dear Maintainer,
I have recently needed to use a python3-only sphinx build process on a
system with both python-sphinx & python3-sphinx co-installed. IMHO
co-installation
could be a little cleaner and easier if sphinx:
- Used update-alternatives to provide /usr/bin/sphinx-* in a
configurable way. (e.g similar to how docutils handles this problem). This
could use the current script installation path under
/usr/share/sphinx/scripts/python*/
- Or, installed binaries under /usr/bin with the suffix '3', i.e. install
/usr/bin/sphinx-build3. (modelled after pip/pip3 & nosetests/nosetests3 and
other similar examples)
- Or, a combination of both these, where python-sphinx and
python3-sphinx install /usr/bin/sphinx-*{2,3} respectively, and
update-alternatives is used to provide /usr/bin/sphinx-* without
prefix.
Is there any reason that one of these approaches have not been taken? I'm
relatively new to Debian packaging so there may be subtlety here I'm
missing.
I'm happy to have a go at implementing a solution to this myself, given
guidance as to the best option to implement (if any).
Cheers,
Kevin
P.S., I know one can always do /usr/share/sphinx/scripts/python3/sphinx-build
as a workaround.
-- System Information:
Debian Release: stretch/sid
APT prefers testing
APT policy: (900, 'testing'), (500, 'testing-updates'), (500,
'stable-updates'), (400, 'unstable'), (300, 'stable')
Architecture: amd64 (x86_64)
Kernel: Linux 4.3.0-1-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
---
Kevin Murray
0xA4B4EE6A
Bug#813840: ITP: libqcpp -- A C++ library for next-gen sequencing data quality control.
Package: wnpp Severity: wishlist Owner: Kevin Murray <s...@kdmurray.id.au> * Package name: libqcpp Version : 0.1.9 Upstream Author : Kevin Murray <s...@kdmurray.id.au> * URL : https://github.com/kdmurray91/libqcpp * License : LGPL Programming Lang: C++ Description : A C++ library for next-gen sequencing data quality control. libqc++ implements adaptor trimming, windowed quality trimming, length filtering and trimming, format conversion, and basic read manipulation. It also provides classes for implementation of new measures and easy creation of bespoke filtering tools. Some tools are packaged of the source package libqcpp, including gbsqc, a tool specifically for quality control of genotyping by sequencing. This package will be maintained under the Debian Med team. --- Kevin Murray 0xA4B4EE6A
Bug#811099: scrm: FTBFS on *i386: test suite fails
Hi Aaron, Thanks for the report. This looks like mixed use of size_t and fixed with integral types. Sorry, but I don't have time to investigate right now, but will do so in about a week. If anyone else wants to jump in they are of course more than welcome. Cheers, Kevin On 11:54 15/01, Aaron M. Ucko wrote: > Source: scrm > Version: 1.6.1-1 > Severity: important > Justification: fails to build from source > > Builds of scrm for i386, hurd-i386, and kfreebsd-i386 all encountered > identical test suite errors: > > test_model.cc:156:Assertion > Test name: TestModel::testAddPopulationSizes > assertion failed > - Expression: model.population_size(0) == 5 > > test_param.cc:182:Assertion > Test name: TestParam::testParseCommonOptions > assertion failed > - Expression: areSame(model.default_pop_size, > (size_t)model.population_size(2)) > > test_summary_statistics.cc:258:Assertion > Test name: TestSummaryStatistics::testOrientedForestGenerateTreeData > assertion failed > - Expression: of.heights_.at(6) == 10.0 * sf && of.parents_.at(6) == 0 > > Failures !!! > Run: 111 Failure total: 3 Failures: 3 Errors: 0 > make[1]: *** [unittests] Error 1 > > Could you please take a look? > > Thanks! > --- Kevin Murray 0xA4B4EE6A
Bug#810583: libeigen3-doc: Navbar obscures documentation pages in HTML docs
Hi Anton, On 09:48 10/01, Anton Gladky wrote: > Hi Kevin, > > as far as I can see [0] shows the same version which is > displayed on a local documentation, 3.2.92. The number > 3.2 will be changed on 3.3 only when a a stable 3.3 will be > released. Thanks for looking into this. That makes sense, now you mention it. Cheers, Kevin --- Kevin Murray 0xA4B4EE6A
Bug#810576: ITP: hail -- Efficiently extract arbitrary lines from a file or stream
Package: wnpp Severity: wishlist Owner: Kevin Murray <s...@kdmurray.id.au> * Package name: hail Version : 0.1.1 Upstream Author : Kevin Murray * URL : https://github.com/kdmurray91/hail * License : GPL Programming Lang: C Description : Efficiently extract arbitrary lines from a file or stream Hail gets its name from a contraction of head and tail, the common alternative to this program. It extracts lines from a file, taken on stdin, and prints them on stdout. It's so simple that the Unix wizards of old never bothered. Hail will be co-maintained in the Debian Med team.
Bug#810583: libeigen3-doc: Navbar obscures documentation pages in HTML docs
Package: libeigen3-doc Version: 3.3~beta1-1 Severity: normal Dear Maintainer, When viewing the HTML documentation pages, a grey box (which should contain the navbar) obscures the text of the page. In addition, the version displayed does not correspond to the package version (documentation says 3.2.92, eigen version is 3.3~beta1). A screen shot of the specified behaviour is available at [0]. It should also be possible to show this by visiting [1] on a system with libeigen3-doc installed. [0]: http://imgur.com/gallery/kX3RC9R [1]: file:///usr/share/doc/libeigen3-doc/html/index.html Cheers, Kevin -- System Information: Debian Release: stretch/sid APT prefers unstable APT policy: (900, 'unstable'), (500, 'oldstable'), (400, 'testing'), (300, 'stable'), (1, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.3.0-1-amd64 (SMP w/4 CPU cores) Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages libeigen3-doc depends on: ii fonts-freefont-ttf [ttf-freefont] 20120503-4 ii libjs-jquery 1.11.3+dfsg-4 libeigen3-doc recommends no packages. Versions of packages libeigen3-doc suggests: ii libeigen3-dev 3.3~beta1-1 -- no debconf information
Bug#809972: ITP: scrm -- A coalescent simulator for genome-scale sequences
Package: wnpp Severity: wishlist Owner: Kevin Murray <s...@kdmurray.id.au> * Package name: scrm Version : 1.6.1 Upstream Author : Paul R. Staab <deve...@paulstaab.de> * URL : https://github.com/scrm/scrm * License : GPL Programming Lang: C++ Description : A coalescent simulator for genome-scale sequences scrm simulates the evolution of genetic sequences. It takes a neutral evolutionary model as input, and generates random sequences that evolved under the model. As coalescent simulator, it traces the ancestry of the sampled sequences backwards in time and is therefore extremely efficient. Compared to other coalescent simulators, it can simulate chromosome-scale sequences without a measurable reduction of genetic linkage between different sites. This package will be maintained by the Debian Med team.
Bug#808710: libqes: FTBFS on platforms with unsigned char
Source: libqes Version: 0.1.20-1 Severity: important Tags: upstream Dear Maintainer, An upstream bug causes a test failure on systems with char == unsigned char (e.g. ARM). Importing the new upstream release 0.1.21 should fix this issue. Cheers, K -- System Information: Debian Release: stretch/sid APT prefers unstable APT policy: (900, 'unstable'), (500, 'oldstable'), (400, 'testing'), (300, 'stable'), (1, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.3.0-1-amd64 (SMP w/4 CPU cores) Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system)
Bug#808424: [Debian-med-packaging] Bug#808424: [Bug#808424: khmer: FTBFS: assumes a real home directory]
Hi all, On 10:34 21/12, Andreas Tille wrote: > Hi Michael, > > I see several suspicious lintian warnings: > I'm actually working on this now. I noticed the same issue when trying to fix another issue: liboxli-dev doesn't depend on liboxli1. I will push my work on both now, thought it's not ready for upload. Cheers, Kevin --- Kevin Murray 0xA4B4EE6A
Bug#808570: FTBFS: upstream bug causing FTBFS on i386
Package: axe-demultiplexer Version: 0.3.0+dfsg-2 Severity: important Tags: upstream Dear Maintainer, An upstream bug prevents tests passing on 32-bit systems. Upstream has fixed this in the latest release. Cheers, Kevin -- System Information: Debian Release: stretch/sid APT prefers unstable APT policy: (900, 'unstable'), (500, 'oldstable'), (400, 'testing'), (300, 'stable'), (1, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.3.0-1-amd64 (SMP w/4 CPU cores) Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages axe-demultiplexer depends on: ii libc62.21-4 ii libgsl2 2.1+dfsg-2 ii libqes0 0.1.20-1 axe-demultiplexer recommends no packages. axe-demultiplexer suggests no packages. -- no debconf information
Bug#806594: python-skbio: issues fixed, upload required
Hi all, On 13:22 21/12, Kevin Murray wrote: > Hi Andreas, > > On 09:07 06/12, Andreas Tille wrote: > > Hi Kevin, > > > > any news about building the docs? I have reset the target distribution to > > UNRELEASED since it does not build in a pbuilder chroot. > > > > I'm still stuck on this one. Does someone with more Debian python knowledge > than > I want to have a look? I'm sure it's some silly oversight on my behalf, but I > seem to be having issues with PYTHONPATH during the build of the docs (the > skbio module is imported by sphinx's conf.py). My latest attempt is pushed to: > > ssh://git.debian.org/git/debian-med/python-skbio.git > I've fixed the issues I was having after I worked out how to drop to a shell. Could I please get someone to upload this package? --- Kevin Murray 0xA4B4EE6A
Bug#806594: [Debian-med-packaging] Skbio upload?
Hi Andreas, On 09:07 06/12, Andreas Tille wrote: > Hi Kevin, > > any news about building the docs? I have reset the target distribution to > UNRELEASED since it does not build in a pbuilder chroot. > I'm still stuck on this one. Does someone with more Debian python knowledge than I want to have a look? I'm sure it's some silly oversight on my behalf, but I seem to be having issues with PYTHONPATH during the build of the docs (the skbio module is imported by sphinx's conf.py). My latest attempt is pushed to: ssh://git.debian.org/git/debian-med/python-skbio.git Thanks! Cheers, Kevin --- Kevin Murray 0xA4B4EE6A
Bug#716357: [Mayhem] Bug report on filo: stats crashes with exit status 139
Hi all, I'm working on this bug to find the root of the issue and fix it. Cheers, Kevin --- Kevin Murray 0xA4B4EE6A
Bug#806767: ITP: libzstd -- fast lossless compression algorithm, targeting real-time compression scenarios
Hi Tiago and Konstantin You are both correct, yes. Sorry, and thanks for correcting this (though it's correct in d/control and d/copyright). Cheers, K On 11:41 01/12, Tiago Ilieve wrote: > Kevin, > > On 1 December 2015 at 00:33, Kevin Murray <s...@kdmurray.id.au> wrote: > > Package: wnpp > > Severity: wishlist > > Owner: Kevin Murray <s...@kdmurray.id.au> > > > > * Package name: libzstd > > Version : 0.4.0 > > Upstream Author : Yann Collet > > * URL : https://github.com/Cyan4973 > > * License : BSD > > Programming Lang: C > > Description : fast lossless compression algorithm > > The actual URL is https://github.com/Cyan4973/zstd , right? > > Regards, > Tiago. > > -- > Tiago "Myhro" Ilieve > Blog: https://blog.myhro.info/ > GitHub: https://github.com/myhro > LinkedIn: https://br.linkedin.com/in/myhro > Montes Claros - MG, Brasil > --- Kevin Murray GPG pubkey: http://www.kdmurray.id.au/static/A4B4EE6A.asc FPR: 656C 0632 1EAB 2C3F 3837 9767 17C2 8EB1 A4B4 EE6A
Bug#806828: ITP: dawg -- program to simulate the evolution of recombinant DNA sequences
Package: wnpp Severity: wishlist Owner: Kevin Murray <s...@kdmurray.id.au> * Package name: dawg Version : 1.2.0 Upstream Author : Reed A. Cartwright * URL : http://scit.us/projects/dawg * License : GPL-2 Programming Lang: C++ Description : program to simulate the evolution of recombinant DNA sequences DNA Assembly with Gaps (Dawg) is an application designed to simulate the evolution of recombinant DNA sequences in continuous time based on the robust general time reversible model with gamma and invariant rate heterogeneity and a novel length-dependent model of gap formation. The application accepts phylogenies in Newick format and can return the sequence of any node, allowing for the exact evolutionary history to be recorded at the discretion of users. Dawg records the gap history of every lineage to produce the true alignment in the output. Many options are available to allow users to customize their simulations and results.
Bug#806767: ITP: libzstd -- fast lossless compression algorithm, targeting real-time compression scenarios
Package: wnpp Severity: wishlist Owner: Kevin Murray <s...@kdmurray.id.au> * Package name: libzstd Version : 0.4.0 Upstream Author : Yann Collet * URL : https://github.com/Cyan4973 * License : BSD Programming Lang: C Description : fast lossless compression algorithm Zstd, short for Zstandard, is a fast lossless compression algorithm, targeting real-time compression scenarios at zlib-level compression ratio. Zstd can also offer stronger compression ratio at the cost of compression speed. Speed / Ratio trade-off is configurable by small increment, to fit different situations. Note however that decompression speed is preserved and remain roughly the same at all settings, a property shared by most LZ compression algorithms, such as zlib. This will be co-maintained under Debian Med.
Bug#806594: python-skbio: No documentation packaged
Package: python-skbio Version: 0.4.0-3 Severity: normal Tags: patch Hi all, I noticed today that scikit-bio (python-skbio in Debian) has no documentation packaged, despite upstream having quite rich Sphinx documentation. I'm fixing this, and will push to git soon (patch not so much attached as incoming :]). Cheers, Kevin -- System Information: Debian Release: stretch/sid APT prefers unstable APT policy: (900, 'unstable'), (500, 'oldstable'), (400, 'testing'), (300, 'stable'), (1, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.2.0-1-amd64 (SMP w/4 CPU cores) Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages python-skbio depends on: ii ipython 2.3.0-2 ii libc62.19-22 ii python 2.7.9-1 ii python-bz2file 0.98-1 ii python-cachecontrol 0.11.5-1.1 ii python-contextlib2 0.4.0-3 ii python-decorator 4.0.2-1 ii python-future0.15.2-1 ii python-matplotlib1.5.0~rc2-1 ii python-natsort 4.0.3-2 ii python-numpy 1:1.9.2-5 ii python-pandas0.17.0+git8-gcac4ad2-2 ii python-scipy 0.16.1-1 ii python-six 1.10.0-1 pn python:any python-skbio recommends no packages. python-skbio suggests no packages. -- no debconf information
Bug#805153: ITP: libqes -- a next-gen sequencing format parsing and utility library for C
Package: wnpp Severity: wishlist Owner: Kevin Murray <s...@kdmurray.id.au> * Package name: libqes Version : 0.1.20 Upstream Author : Kevin Murray <s...@kdmurray.id.au> * URL : https://github.com/kdmurray91/libqes * License : GPL-3+ Programming Lang: C Description : Next-gen sequencing format parsing and utility library for C This is packaged as a build-dep of the Axe demultiplexer (src pkg axe-demultiplexer). It will be co-maintained with Debian Med.
Bug#804646: ITP: partitionfinder -- programs for simultaneously choosing partitioning schemes and models of molecular evolution for sequence data.
X-Debbugs-CC: Debian Med Packaging <debian-med-packag...@lists.alioth.debian.org> Package: wnpp Severity: wishlist Owner: Kevin Murray <s...@kdmurray.id.au> * Package name: partitionfinder Version : 2.0.0 Upstream Author : Brett Calcott and Rob Lanfear * URL : https://github.com/brettc/partitionfinder * License : GPL-3+ Programming Lang: Python Description : programs for simultaneously choosing partitioning schemes and models of molecular evolution for sequence data. PartitionFinder is a series of programs for simultaneously choosing partitioning schemes and models of molecular evolution for sequence data. You can use them before running a phylogenetic analysis, in order to decide how to divide up your sequence data into separate blocks before analysis, and to simultaneously perform model selection on each of those blocks. This package will be co-maintained under Debian Med. --- Kevin Murray GPG pubkey: http://www.kdmurray.id.au/static/A4B4EE6A.asc FPR: 656C 0632 1EAB 2C3F 3837 9767 17C2 8EB1 A4B4 EE6A
Bug#801900: axe-demultiplexer: /usr/bin/axe already used by the axe package
Hi Andreas, On 17:56 27/10, Andreas Tille wrote: > Hi Kevin, > > do you have a plan to work on this? I'd recommend to choose the name > > /usr/bin/axe-demultiplexer > > and provide > > /usr/lib/debian-med/bin/axe > > in addition and add > > Recommends: med-config (>= 2.1) > > to d/control. This could be completed by and according hint in > debian/README.Debian. You might like to have a look into the packages > inspect, libgenome-perl or plink as examples. Feel free to ask for > further advise. > Sorry, I thought I responded to this already. I'm fixing this upstream so that the binary name doesn't change; it will now be `axe-demux` everywhere. I've re-released. I've decided to re-do the entire packaging too, so that we don't bundle libqes or a cut-down gsl. I have a couple of questions about this but I'll as those in a separate email. Cheers, Kevin --- Kevin Murray GPG pubkey: http://www.kdmurray.id.au/static/A4B4EE6A.asc FPR: 656C 0632 1EAB 2C3F 3837 9767 17C2 8EB1 A4B4 EE6A
Bug#803009: dwgsim: Binary is not included in package
Package: dwgsim Version: 0.1.11-1 Severity: grave Justification: renders package unusable Hi all, I somehow managed not to add the debian/dwgsim.install file to git. Due to the upstream makefile not having an install rule, this lead to a Debian package with no binary. I have fixed this in git. Mea culpa, Sorry! Cheers, Kevin -- System Information: Debian Release: stretch/sid APT prefers unstable APT policy: (900, 'unstable'), (500, 'oldstable'), (400, 'testing'), (300, 'stable'), (1, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.2.0-1-amd64 (SMP w/4 CPU cores) Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) -- no debconf information
Bug#801307: ITP: pybtex-docutils -- A docutils backend for pybtex
Hi Sandro On 18:35 17/10, Sandro Tosi wrote: > I think you should consider packaging it under DPMT as it has > potential (and even real) applications in other packages. of course > seqan belongs to deb-med, I do think that a general py module should > belong to a general py module team. > OK, sure, I'll contact the DPMT about this and the remainder of the python modules needed to build seqan's docs. Cheers, Kevin --- Kevin Murray GPG pubkey: http://www.kdmurray.id.au/static/A4B4EE6A.asc FPR: 656C 0632 1EAB 2C3F 3837 9767 17C2 8EB1 A4B4 EE6A
Bug#800358: ITP: python-sphinxcontrib.bibtex -- allows the use of Bibtex citations in sphinx documentation
Hi Sandro, On 18:36 17/10, Sandro Tosi wrote: > Hey Kevin, > any update on this? I needs this package to build networkx > documentation. If you need help or a sponsor (even with the other deps > packages), please let me know. It would be even better if you decide > to package to package it under DPMT umbrella > I think this is just waiting on some of its dependencies I'm packaging. I'll contact the DPMT about co-maintainership. I think they are all ready for review, though there are probably issues to address. Cheers, Kevin --- Kevin Murray GPG pubkey: http://www.kdmurray.id.au/static/A4B4EE6A.asc FPR: 656C 0632 1EAB 2C3F 3837 9767 17C2 8EB1 A4B4 EE6A
Bug#801696: axe-demultiplexer: FTBFS: suite fails on most architectures
Hi Aaron, I'm both the Debian packager and upstream, so I'll take this on. It's almost certainly an upstream issue in the unit tests. I don't test on anything other than amd64 Debian unfortunately. Cheers, K --- Kevin Murray GPG pubkey: http://www.kdmurray.id.au/static/A4B4EE6A.asc FPR: 656C 0632 1EAB 2C3F 3837 9767 17C2 8EB1 A4B4 EE6A
Bug#801658: [Debian-med-packaging] Bug#801658: python-skbio: Please build python3-skbio for all supported python3 versions
Hi Scott, On 01:27 13/10, Scott Kitterman wrote: > Package: python-skbio > > Packages that are only built for the default python3 version become > temporarily uninstallable when the default version changes. We can do > transitions much more smoothly if the package is built for all supported > versions. > > Please see the attached patch. We are almost finished with the transition > that adds python3.5 as a supported python3 version and hope to switch the > default python3 from python3.4 to python3.5 soon. If you could upload this > soonish, it would aid making the switch smoother. > > Thanks, > > Scott K I've applied the patch and added a (Closes: ) in d/changelog. Can a DD upload please? Cheers, Kevin --- Kevin Murray GPG pubkey: http://www.kdmurray.id.au/static/A4B4EE6A.asc FPR: 656C 0632 1EAB 2C3F 3837 9767 17C2 8EB1 A4B4 EE6A
Bug#801307: ITP: pybtex-docutils -- A docutils backend for pybtex
Hi Sandro, On 12:47 08/10, Sandro Tosi wrote: [...] > > > > This package will be co-maintained with the Debian Med team. > > why in Deb Med team and not a more general python team like DPMT? It > doesnt look like it has anything specific to "med" > My rationale is that no-one in such teams has packaged it yet, and I am only packaging it as a build-depend of SeqAn, which is very much a Debian Med package. Though I understand if the team would rather this be maintained elsewhere. Cheers, K --- Kevin Murray GPG pubkey: http://www.kdmurray.id.au/static/A4B4EE6A.asc FPR: 656C 0632 1EAB 2C3F 3837 9767 17C2 8EB1 A4B4 EE6A
Bug#801306: ITP: python-oset -- An ordered set data structure for Python
Package: wnpp Severity: wishlist Owner: Kevin Murray <s...@kdmurray.id.au> * Package name: python-oset Version : 0.1.3 Upstream Author : Carlos Martin, Raymond Hettinger * URL : https://gitorious.com/sleipnir/python-oset * License : BSD Programming Lang: Python Description : An ordered set data structure for Python A set data structure that remembers original insertion order. The implementation based on a doubly linked link and an internal dictionary. This design gives OrderedSet the same big-Oh running times as regular sets including O(1) adds, removes, and lookups as well as O(n) iteration. This is a dependency of sphinxcontrib-bibtex, which is required to build seqan's documentation. This package will be co-maintained in the Debian Med team.
Bug#801307: ITP: pybtex-docutils -- A docutils backend for pybtex
Package: wnpp Severity: wishlist Owner: Kevin Murray <s...@kdmurray.id.au> * Package name: pybtex-docutils Version : 0.2.1 Upstream Author : Matthias C. M. Troffaes * URL : https://github.com/mcmtroffaes/pybtex-docutils * License : Expat Programming Lang: Python Description : A docutils backend for pybtex Pybtex is a drop-in replacement for BibTeX written in Python. pybtex-docutils is a docutils backend for pybtex. pybtex-docutils is a dependency for sphinxcontrib-bibtex, required for the build of seqan's documentation. This package will be co-maintained with the Debian Med team.
Bug#801309: ITP: python-latexcodec -- A lexer and codec to work with LaTeX code in Python.
Package: wnpp Severity: wishlist Owner: Kevin Murray <s...@kdmurray.id.au> * Package name: python-latexcodec Version : 1.0.1 Upstream Author : Matthias C. M. Troffaes * URL : https://github.com/mcmtroffaes/pybtex-docutils * License : Expat Programming Lang: Python Description : A lexer and codec to work with LaTeX code in Python. A dependency of the sphinxcontrib-bibtex package. This will be co-maintained with the Debian Med team.
Bug#800358: ITP: python-sphinxcontrib.bibtex -- allows the use of Bibtex citations in sphinx documentation
Package: wnpp Severity: wishlist Owner: Kevin Murray <s...@kdmurray.id.au> * Package name: python-sphinxcontrib.bibtex Version : 0.3.2 Upstream Author : Matthias C. M. Troffaes * URL : https://github.com/mcmtroffaes/sphinxcontrib-bibtex/blob/develop/LICENSE.rst * License : BSD Programming Lang: Python Description : allows the use of Bibtex citations in sphinx documentation This sphinx extension allows the use of Bibtex citations in sphinx documentation. It will be packaged into both py2 and py3 packages. I will co-maintain this as part of the Debian Med packaging team. It is required to build the documentation of, e.g., seqan.
Bug#799830: ITP: dwgsim -- DWGSIM is an improved short read simulator
Package: wnpp Severity: wishlist Owner: Kevin Murray <s...@kdmurray.id.au> * Package name: dwgsim Version : 0.1.11 Upstream Author : Nils Homer * URL : https://github.com/nh13/DWGSIM * License : GPLv2, MIT/X Programming Lang: C Description : DWGSIM: an improved short read simulator DWGSIM is a whole-genome shotgun sequencing read simulator. It simulates reads from Illuima, SOLiD and Ion Torrent platforms. This package will be maintained by the Debian Med Packaging Team.
Bug#798824: ITP: snakemake -- a pythonic workflow system
Package: wnpp Severity: wishlist Owner: Kevin Murray <s...@kdmurray.id.au> * Package name: snakemake Version : 3.4 Upstream Author : Johannes Köster <johannes.koes...@tu-dortmund.de> * URL : https://bitbucket.org/johanneskoester/snakemake * License : MIT Programming Lang: Python Description : Snakemake -- a pythonic workflow system >From upstream's README: Build systems like GNU Make are frequently used to create complicated workflows, e.g. in bioinformatics. This project aims to reduce the complexity of creating workflows by providing a clean and modern domain specific specification language (DSL) in python style, together with a fast and comfortable execution environment. This will be collaboratively maintained with the Debian Med team. Cheers! --- Kevin Murray
Bug#794088: ITP: axe-demultiplexer -- demultiplexes DNA sequencing reads based upon 5' read barcodes
Package: wnpp Severity: wishlist Owner: Kevin Murray s...@kdmurray.id.au * Package name: axe-demultiplexer Version : 0.2.8 Upstream Author : Kevin Murray s...@kdmurray.id.au * URL : https://github.com/kdmurray91/axe * License : GPL3+ Programming Lang: C Description : Axe demultiplexes DNA sequencing reads based upon 5' read barcodes Axe very rapidly selects the optimal barcode present in a sequence read, even in the presence of sequencing errors. The algorithm is able to handle combinatorial barcoding, barcodes of differing length, and several mismatches per barcode. As I am the upstream author, I'm not sure what Debian Med policy is regarding uploader-ship. But I have prepared a Debian package. -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#792188: sphinxcontrib-autoprogram: Create a python3-sphinxcontrib.autoprogram package
Package: sphinxcontrib-autoprogram Version: 0.1.1-1 Severity: important Hi all, The python3 packaging of khmer will need a python3 version of sphinxcontrib.autoprogram. This is a bug to let you know that I'm working on this. Cheers, Kevin -- System Information: Debian Release: stretch/sid APT prefers unstable APT policy: (500, 'unstable'), (500, 'testing'), (500, 'stable'), (500, 'oldstable'), (1, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.0.0-2-amd64 (SMP w/4 CPU cores) Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages sphinxcontrib-autoprogram depends on: ii python 2.7.9-1 ii python-sphinx 1.2.3+dfsg-1 sphinxcontrib-autoprogram recommends no packages. sphinxcontrib-autoprogram suggests no packages. -- no debconf information -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#791873: [Debian-med-packaging] Bug#791873: wgsim already included within samtools
Charles, On 09:23 10/07, Charles Plessy wrote: Le Thu, Jul 09, 2015 at 04:15:35PM +1000, Kevin Murray a écrit : Package: wgsim Severity: serious Justification: Policy 7.6.1 Hi all, I have inadvertently packaged wgsim for Debian without realising that it already is packaged in a different form as part of the samtools source package. For this reason, I'd like to withdraw the wgsim (source and binary) package and offer my apologies for not having inspected samtools throughly. Hi Kevin and everybody, interstingly, the question of which wgsim is canonical has been asked yesterday on GitHub's issue tracker (Hi Shaun, are you still reading us on this list ?). I added a comment saying that Debian is interested in the answer. https://github.com/samtools/samtools/issues/429 Yes, I saw that, thanks. I was under the impression that what Shaun said was correct and that is had been deprecated and removed from samtools as part of their 1.0 release. But I was wrong at least as far as its removal is concerned. Cheers, Kevin --- Kevin Murray GPG pubkey: http://www.kdmurray.id.au/static/A4B4EE6A.asc FPR: 656C 0632 1EAB 2C3F 3837 9767 17C2 8EB1 A4B4 EE6A -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#791873: wgsim already included within samtools
Package: wgsim Severity: serious Justification: Policy 7.6.1 Hi all, I have inadvertently packaged wgsim for Debian without realising that it already is packaged in a different form as part of the samtools source package. For this reason, I'd like to withdraw the wgsim (source and binary) package and offer my apologies for not having inspected samtools throughly. Kevin Murray -- System Information: Debian Release: stretch/sid APT prefers unstable APT policy: (500, 'unstable'), (500, 'testing'), (500, 'stable'), (500, 'oldstable'), (1, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 4.0.0-2-amd64 (SMP w/4 CPU cores) Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#791395: ITP: wgsim -- Simulate whole-genome sequencing data
package: wnpp Severity: wishlist Owner: 'Kevin Murray' s...@kdmurray.id.au *Package Name : wgsim Version : 0.3.1-r13 Upstream Author : Heng Li *URL : https://github.com/lh3/wgsim *License : MIT *Description : wgsim simulates sequencing reads from a reference genome. Wgsim is a small tool for simulating sequence reads from a reference genome. It is able to simulate diploid genomes with SNPs and insertion/deletion (INDEL) polymorphisms, and simulate reads with uniform substitution sequencing errors. It does not generate INDEL sequencing errors, but this can be partly compensated by simulating INDEL polymorphisms. --- Kevin Murray GPG pubkey: http://www.kdmurray.id.au/static/A4B4EE6A.asc FPR: 656C 0632 1EAB 2C3F 3837 9767 17C2 8EB1 A4B4 EE6A -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
Bug#776539: RFS: scythe/0.994-1 [ITP] -- Bayesian adaptor trimmer for sequencing reads
Package: sponsorship-requests Severity: wishlist Dear mentors, I am looking for a sponsor for my package scythe * Package name: scythe Version : 0.994-1 Upstream Author : Vince Buffalo * URL : https://github.com/vsbuffalo/scythe * License : Expat Section : science It builds these binary packages: scythe - Bayesian adaptor trimmer for sequencing reads To access further information about this package, please visit the following URL: http://mentors.debian.net/package/scythe Alternatively, one can download the package with dget using this command: dget -x http://mentors.debian.net/debian/pool/main/s/scythe/scythe_0.994-1.dsc I'm new to Debian packaging/development, and I'd like to start by packaging a useful piece of software for those using Debian in computational biology. Scythe uses a Naïve Bayesian matching algorithm to trim contaminants from sequencing reads. It is more accurate than other similar packages due to the probabilistic matching algorithm that it uses, which accounts for features of common DNA sequencing platforms. I have previously contributed code to scythe, and I believe I am sufficiently familiar with its development and code base to maintain this package. I've made the package, and uploaded it to mentors.debian.net (see above dget/webpage links). Please let me know how I can improve! Thanks, Kevin Murray s...@kdmurray.id.au I'm an FSF member -- Help us support software freedom! https://www.fsf.org/join GPG pubkey: http://www.kdmurray.id.au/static/A4B4EE6A.asc FPR: 656C 0632 1EAB 2C3F 3837 9767 17C2 8EB1 A4B4 EE6A signature.asc Description: Digital signature
Bug#776179: ITP: scythe -- Bayesian adaptor trimmer for sequencing reads
package: wnpp Severity: wishlist Owner: 'Kevin Murray' s...@kdmurray.id.au *Package Name : scythe Version : 0.994-1 Upstream Author : Vince Buffalo *URL : https://github.com/vsbuffalo/scythe *License : MIT *Description : Bayesian adaptor trimmer for sequencing reads I am packaging as it is a frequently used packing in computational biology. --- Kevin Murray s...@kdmurray.id.au -- To UNSUBSCRIBE, email to debian-bugs-dist-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org
