[med-svn] [Git][med-team/forester][upstream] New upstream version 0.0+20180205

[Andreas Tille]

Andreas Tille pushed to branch upstream at Debian Med / forester


Commits:
75215540 by Andreas Tille at 2018-02-12T08:20:36+01:00
New upstream version 0.0+20180205
- - - - -


30 changed files:

- forester/java/build.xml
- forester/java/classes/com/itextpdf/text/Anchor.class
- forester/java/classes/com/itextpdf/text/BaseColor.class
- forester/java/classes/com/itextpdf/text/Chapter.class
- forester/java/classes/com/itextpdf/text/Chunk.class
- forester/java/classes/com/itextpdf/text/DocWriter.class
- forester/java/classes/com/itextpdf/text/Document.class
- forester/java/classes/com/itextpdf/text/DocumentException.class
- forester/java/classes/com/itextpdf/text/Element.class
- forester/java/classes/com/itextpdf/text/Font.class
- forester/java/classes/com/itextpdf/text/FontFactoryImp.class
- forester/java/classes/com/itextpdf/text/GreekList.class
- forester/java/classes/com/itextpdf/text/Image.class
- forester/java/classes/com/itextpdf/text/Jpeg.class
- forester/java/classes/com/itextpdf/text/Jpeg2000.class
- forester/java/classes/com/itextpdf/text/LICENSE.txt
- forester/java/classes/com/itextpdf/text/List.class
- forester/java/classes/com/itextpdf/text/ListItem.class
- forester/java/classes/com/itextpdf/text/MarkedObject.class
- forester/java/classes/com/itextpdf/text/MarkedSection.class
- forester/java/classes/com/itextpdf/text/NOTICE.txt
- forester/java/classes/com/itextpdf/text/PageSize.class
- forester/java/classes/com/itextpdf/text/Paragraph.class
- forester/java/classes/com/itextpdf/text/Phrase.class
- forester/java/classes/com/itextpdf/text/Rectangle.class
- forester/java/classes/com/itextpdf/text/RomanList.class
- forester/java/classes/com/itextpdf/text/Section.class
- forester/java/classes/com/itextpdf/text/Utilities.class
- forester/java/classes/com/itextpdf/text/ZapfDingbatsList.class
- forester/java/classes/com/itextpdf/text/ZapfDingbatsNumberList.class


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/forester/commit/752155402bcb354f1cb373d6600aeb86a4f9e878

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[med-svn] [Git][med-team/forester] Pushed new tag upstream/0.0+20180205

[Andreas Tille]

Andreas Tille pushed new tag upstream/0.0+20180205 at Debian Med / forester

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[med-svn] [Git][med-team/forester][master] 4 commits: Add get-orig-source to fetch latest upstream as long as…

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / forester


Commits:
3cad3a6d by Andreas Tille at 2018-02-12T08:19:43+01:00
Add get-orig-source to fetch latest upstream as long as 
https://github.com/cmzmasek/forester/issues/17 is not fixed

- - - - -
75215540 by Andreas Tille at 2018-02-12T08:20:36+01:00
New upstream version 0.0+20180205
- - - - -
cacd679c by Andreas Tille at 2018-02-12T08:21:19+01:00
Update upstream source from tag upstream/0.0+20180205

Update to upstream version 0.0+20180205
with Debian dir 34434498a0a4e99e35a216a454f772178ef2cb9e
- - - - -
06a6b7b7 by Andreas Tille at 2018-02-12T08:26:37+01:00
New upstream commit

- - - - -


30 changed files:

- debian/changelog
- debian/get-orig-source
- forester/java/build.xml
- forester/java/classes/com/itextpdf/text/Anchor.class
- forester/java/classes/com/itextpdf/text/BaseColor.class
- forester/java/classes/com/itextpdf/text/Chapter.class
- forester/java/classes/com/itextpdf/text/Chunk.class
- forester/java/classes/com/itextpdf/text/DocWriter.class
- forester/java/classes/com/itextpdf/text/Document.class
- forester/java/classes/com/itextpdf/text/DocumentException.class
- forester/java/classes/com/itextpdf/text/Element.class
- forester/java/classes/com/itextpdf/text/Font.class
- forester/java/classes/com/itextpdf/text/FontFactoryImp.class
- forester/java/classes/com/itextpdf/text/GreekList.class
- forester/java/classes/com/itextpdf/text/Image.class
- forester/java/classes/com/itextpdf/text/Jpeg.class
- forester/java/classes/com/itextpdf/text/Jpeg2000.class
- forester/java/classes/com/itextpdf/text/LICENSE.txt
- forester/java/classes/com/itextpdf/text/List.class
- forester/java/classes/com/itextpdf/text/ListItem.class
- forester/java/classes/com/itextpdf/text/MarkedObject.class
- forester/java/classes/com/itextpdf/text/MarkedSection.class
- forester/java/classes/com/itextpdf/text/NOTICE.txt
- forester/java/classes/com/itextpdf/text/PageSize.class
- forester/java/classes/com/itextpdf/text/Paragraph.class
- forester/java/classes/com/itextpdf/text/Phrase.class
- forester/java/classes/com/itextpdf/text/Rectangle.class
- forester/java/classes/com/itextpdf/text/RomanList.class
- forester/java/classes/com/itextpdf/text/Section.class
- forester/java/classes/com/itextpdf/text/Utilities.class


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/forester/compare/0524d749f6d21060141854ef7d97b351a574faa0...06a6b7b7072f239f82fb3d0a300643909f593ec8

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[med-svn] [Git][med-team/forester][pristine-tar] pristine-tar data for forester_0.0+20180205.orig.tar.xz

[Andreas Tille]

Andreas Tille pushed to branch pristine-tar at Debian Med / forester


Commits:
d896d3f2 by Andreas Tille at 2018-02-12T08:21:19+01:00
pristine-tar data for forester_0.0+20180205.orig.tar.xz

- - - - -


2 changed files:

- + forester_0.0+20180205.orig.tar.xz.delta
- + forester_0.0+20180205.orig.tar.xz.id


Changes:

=
forester_0.0+20180205.orig.tar.xz.delta
=
Binary files /dev/null and b/forester_0.0+20180205.orig.tar.xz.delta differ


=
forester_0.0+20180205.orig.tar.xz.id
=
--- /dev/null
+++ b/forester_0.0+20180205.orig.tar.xz.id
@@ -0,0 +1 @@
+519bd411c254d2d7483e6e3584ac3ef0e1d24b70



View it on GitLab: 
https://salsa.debian.org/med-team/forester/commit/d896d3f271a0556e87aa8c0e5eda656083579fd5

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[med-svn] [Git][med-team/mummer] Pushed new tag debian/3.23+dfsg-3

[Afif Elghraoui]

Afif Elghraoui pushed new tag debian/3.23+dfsg-3 at Debian Med / mummer

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[med-svn] [Git][med-team/centrifuge] Pushed new tag debian/1.0.3_beta-1

[Andreas Tille]

Andreas Tille pushed new tag debian/1.0.3_beta-1 at Debian Med / centrifuge

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[med-svn] [Git][med-team/obitools][master] Add missing license

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / obitools


Commits:
7e9c4e48 by Andreas Tille at 2018-02-11T23:50:16+01:00
Add missing license

- - - - -


1 changed file:

- debian/copyright


Changes:

=
debian/copyright
=
--- a/debian/copyright
+++ b/debian/copyright
@@ -43,6 +43,23 @@ License: BSD-4-clause
  OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
  OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
+Files: src/obitools/word/_readindex.ext.1.c
+Copyright: 1999 Apple Computer, Inc.
+License: APPLE_LICENSE
+ The contents of this file constitute Original Code as defined in and
+ are subject to the Apple Public Source License Version 1.1 (the
+ "License").  You may not use this file except in compliance with the
+ License.  Please obtain a copy of the License at
+ http://www.apple.com/publicsource and read it before using this file.
+ .
+ This Original Code and all software distributed under the License are
+ distributed on an "AS IS" basis, WITHOUT WARRANTY OF ANY KIND, EITHER
+ EXPRESS OR IMPLIED, AND APPLE HEREBY DISCLAIMS ALL SUCH WARRANTIES,
+ INCLUDING WITHOUT LIMITATION, ANY WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE OR NON-INFRINGEMENT.  Please see the
+ License for the specific language governing rights and limitations
+ under the License.
+
 License: CeCILL-2.1
  CeCILL FREE SOFTWARE LICENSE AGREEMENT
  .



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[med-svn] [Git][med-team/python-bd2k][master] Fix license

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / python-bd2k


Commits:
06d36292 by Andreas Tille at 2018-02-11T23:28:12+01:00
Fix license

- - - - -


1 changed file:

- debian/copyright


Changes:

=
debian/copyright
=
--- a/debian/copyright
+++ b/debian/copyright
@@ -10,7 +10,7 @@ Files: src/bd2k/util/d32.py
src/bd2k/util/d64.py
 Copyright: 2015 Hannes Schmidt 
2014 Dominic Tarr
-License: Apache-2.0
+License: MIT
 
 Files: src/bd2k/util/humanize.py
 Copyright: Giampaolo Rodola 



View it on GitLab: 
https://salsa.debian.org/med-team/python-bd2k/commit/06d362924fb15dc374248394f2e2e9fb82fe404d

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[med-svn] [Git][med-team/python-bd2k][master] Please use `cme fix dpkg-control` in general - specifically to avoid errors like Priority: extra

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / python-bd2k


Commits:
2d27bdb0 by Andreas Tille at 2018-02-11T23:26:13+01:00
Please use `cme fix dpkg-control` in general - specifically to avoid errors 
like Priority: extra

- - - - -


2 changed files:

- debian/changelog
- debian/control


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,4 +1,4 @@
-python-bd2k (1.14~alpha1.43-1) unstable; urgency=medium
+python-bd2k (1.14~alpha1.43-1) UNRELEASED; urgency=medium
 
   [ Michael R. Crusoe ]
   * latest upstream


=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -1,17 +1,22 @@
 Source: python-bd2k
-Section: python
-Priority: extra
 Maintainer: Debian Med Packaging Team 

 Uploaders: Steffen Moeller ,
Michael R. Crusoe 
+Section: python
+Testsuite: autopkgtest-pkg-python
+Priority: optional
 Build-Depends: debhelper (>= 9),
-  dh-python, python-all, python-setuptools, python3-all, python3-setuptools,
-  python-boto,
-  python-dill,
-  python-lockfile,
-  python-mock,
-  python-pytest,
-  python-future
+   dh-python,
+   python-all,
+   python-setuptools,
+   python3-all,
+   python3-setuptools,
+   python-boto,
+   python-dill,
+   python-lockfile,
+   python-mock,
+   python-pytest,
+   python-future
 # Test not performing correctly for python 3.
 #  python-boto, python3-boto,
 #  python-dill, python3-dill,
@@ -19,16 +24,16 @@ Build-Depends: debhelper (>= 9),
 #  python-mock, python3-mock,
 #  python-pytest, python3-pytest
 Standards-Version: 4.1.3
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-bd2k.git/
+Vcs-Git: https://anonscm.debian.org/git/debian-med/python-bd2k.git
 Homepage: https://github.com/BD2KGenomics/bd2k-python-lib
-X-Python-Version: >= 2.6
 #X-Python3-Version: >= 3.2
-Vcs-Git: https://anonscm.debian.org/git/debian-med/python-bd2k.git
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-bd2k.git/
-Testsuite: autopkgtest-pkg-python
+X-Python-Version: >= 2.6
 
 Package: python-bd2k
 Architecture: all
-Depends: ${python:Depends}, ${misc:Depends}
+Depends: ${python:Depends},
+ ${misc:Depends}
 Description: utilities for BD2KGenomics (Python 2)
  This package is a dependency for the toil workflow engine.
  It provides a range of smallish software solutions



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[med-svn] [Git][med-team/porechop][master] 3 commits: Use salsa URLs to not need to add an AliothRewriter rule

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / porechop


Commits:
6b03d9ed by Andreas Tille at 2018-02-11T18:57:45+01:00
Use salsa URLs to not need to add an AliothRewriter rule

- - - - -
4b62c2be by Andreas Tille at 2018-02-11T20:14:38+01:00
Fix installation

- - - - -
8c3917ae by Andreas Tille at 2018-02-11T20:34:52+01:00
Try to add hardening options (seems this does not work)

- - - - -


4 changed files:

- debian/control
- + debian/install
- + debian/links
- debian/rules


Changes:

=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -4,16 +4,18 @@ Uploaders: Cédric Lood 
 Section: science
 Priority: optional
 Build-Depends: debhelper (>= 10),
+   python3-all-dev,
   libseqan2-dev
 Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/pkg-grass/porechop.git
-Vcs-Git: https://anonscm.debian.org/git/pkg-grass/porechop.git
+Vcs-Browser: https://salsa.debian.org/med-team/bandage.git
+Vcs-Git: https://salsa.debian.org/med-team/bandage.git
 Homepage: https://rrwick.github.io/Porechop
 
 Package: porechop
 Architecture: any
 Depends: ${shlibs:Depends},
- ${misc:Depends}
+ ${misc:Depends},
+ ${python3:Depends}
 Description: adapter trimmer for Oxford Nanopore reads
  Porechop is a tool for finding and removing adapters from Oxford
  Nanopore reads. Adapters on the ends of reads are trimmed off, and


=
debian/install
=
--- /dev/null
+++ b/debian/install
@@ -0,0 +1,2 @@
+porechop/*.py  usr/lib/porechop
+porechop/*.so  usr/lib/porechop


=
debian/links
=
--- /dev/null
+++ b/debian/links
@@ -0,0 +1 @@
+usr/lib/porechop/porechop.py   usr/bin/porechop


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -2,5 +2,9 @@
 
 # DH_VERBOSE := 1
 
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+
+include /usr/share/dpkg/default.mk
+
 %:
-   dh $@
+   dh $@ --with python3



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[med-svn] [Git][med-team/cwltool][pristine-tar] 2 commits: pristine-tar data for cwltool_1.0.20180130110340.orig.tar.gz

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch pristine-tar at Debian Med / cwltool


Commits:
f11c4085 by Michael R. Crusoe at 2018-02-11T07:53:20-08:00
pristine-tar data for cwltool_1.0.20180130110340.orig.tar.gz

- - - - -
71646737 by Michael R. Crusoe at 2018-02-11T10:52:26-08:00
pristine-tar data for cwltool_1.0.20180211183944.orig.tar.gz

- - - - -


4 changed files:

- + cwltool_1.0.20180130110340.orig.tar.gz.delta
- + cwltool_1.0.20180130110340.orig.tar.gz.id
- + cwltool_1.0.20180211183944.orig.tar.gz.delta
- + cwltool_1.0.20180211183944.orig.tar.gz.id


Changes:

=
cwltool_1.0.20180130110340.orig.tar.gz.delta
=
Binary files /dev/null and b/cwltool_1.0.20180130110340.orig.tar.gz.delta differ


=
cwltool_1.0.20180130110340.orig.tar.gz.id
=
--- /dev/null
+++ b/cwltool_1.0.20180130110340.orig.tar.gz.id
@@ -0,0 +1 @@
+086a241d34ef7009e8a92f4ee3ab7d90f33b7b82


=
cwltool_1.0.20180211183944.orig.tar.gz.delta
=
Binary files /dev/null and b/cwltool_1.0.20180211183944.orig.tar.gz.delta differ


=
cwltool_1.0.20180211183944.orig.tar.gz.id
=
--- /dev/null
+++ b/cwltool_1.0.20180211183944.orig.tar.gz.id
@@ -0,0 +1 @@
+c537e11e8de072ac91a950190aeede13aef6088a



View it on GitLab: 
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---
View it on GitLab: 
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[med-svn] [Git][med-team/cwltool][upstream] 2 commits: New upstream version 1.0.20180130110340

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch upstream at Debian Med / cwltool


Commits:
098277ff by Michael R. Crusoe at 2018-02-11T07:53:18-08:00
New upstream version 1.0.20180130110340
- - - - -
d729dcc9 by Michael R. Crusoe at 2018-02-11T10:52:24-08:00
New upstream version 1.0.20180211183944
- - - - -


30 changed files:

- Makefile
- PKG-INFO
- README.rst
- cwltool.egg-info/PKG-INFO
- cwltool.egg-info/SOURCES.txt
- + cwltool/argparser.py
- cwltool/builder.py
- cwltool/factory.py
- cwltool/job.py
- cwltool/load_tool.py
- cwltool/main.py
- cwltool/pack.py
- cwltool/process.py
- cwltool/workflow.py
- setup.cfg
- tests/echo.cwl
- tests/override/echo-job-ov.yml
- tests/override/echo-job-ov2.yml
- tests/override/echo-wf.cwl
- tests/override/echo.cwl
- tests/override/ov.yml
- tests/override/ov2.yml
- tests/override/ov3.yml
- tests/random_lines.cwl
- tests/random_lines_mapping.cwl
- tests/seqtk_seq.cwl
- tests/seqtk_seq_with_docker.cwl
- tests/seqtk_seq_wrong_name.cwl
- tests/test_bad_outputs_wf.cwl
- tests/test_examples.py


The diff was not included because it is too large.


View it on GitLab: 
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---
View it on GitLab: 
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[med-svn] [Git][med-team/cwltool][master] 7 commits: New upstream version 1.0.20180130110340

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / cwltool


Commits:
098277ff by Michael R. Crusoe at 2018-02-11T07:53:18-08:00
New upstream version 1.0.20180130110340
- - - - -
99836810 by Michael R. Crusoe at 2018-02-11T07:53:20-08:00
Update upstream source from tag upstream/1.0.20180130110340

Update to upstream version 1.0.20180130110340
with Debian dir 1c0fce0b09e9f05aa0f5002394d3a56a4ea54872
- - - - -
7fc190df by Michael R. Crusoe at 2018-02-11T07:56:49-08:00
1.0.20180130110340

- - - - -
f6019070 by Michael R. Crusoe at 2018-02-11T08:57:58-08:00
Run tests, mark CWL descriptions executable

- - - - -
d729dcc9 by Michael R. Crusoe at 2018-02-11T10:52:24-08:00
New upstream version 1.0.20180211183944
- - - - -
46135acb by Michael R. Crusoe at 2018-02-11T10:52:26-08:00
Update upstream source from tag upstream/1.0.20180211183944

Update to upstream version 1.0.20180211183944
with Debian dir 9e0e50e1a0ea5bf9e5879cdf40c9cab60612fe5e
- - - - -
872dd01e by Michael R. Crusoe at 2018-02-11T11:01:07-08:00
1.0.20180211183944

- - - - -


30 changed files:

- Makefile
- PKG-INFO
- README.rst
- cwltool.egg-info/PKG-INFO
- cwltool.egg-info/SOURCES.txt
- + cwltool/argparser.py
- cwltool/builder.py
- cwltool/factory.py
- cwltool/job.py
- cwltool/load_tool.py
- cwltool/main.py
- cwltool/pack.py
- cwltool/process.py
- cwltool/workflow.py
- debian/changelog
- + debian/clean
- debian/control
- − debian/patches/ignore_cwltest.patch
- debian/rules
- + debian/tests/control
- + debian/tests/run-tests
- setup.cfg
- tests/echo.cwl
- tests/override/echo-job-ov.yml
- tests/override/echo-job-ov2.yml
- tests/override/echo-wf.cwl
- tests/override/echo.cwl
- tests/override/ov.yml
- tests/override/ov2.yml
- tests/override/ov3.yml


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/cwltool/compare/cc25045db379242948062061643fb567f08ffd6b...872dd01ebb2c5197df9fa1558e351e3837a77b85

---
View it on GitLab: 
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[med-svn] [Git][med-team/cwltool] Pushed new tag upstream/1.0.20171017195544

[Michael R. Crusoe]

Michael R. Crusoe pushed new tag upstream/1.0.20171017195544 at Debian Med / 
cwltool

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[med-svn] [Git][med-team/cwltool] Pushed new tag debian/1.0.20180211183944-1

[Michael R. Crusoe]

Michael R. Crusoe pushed new tag debian/1.0.20180211183944-1 at Debian Med / 
cwltool

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[med-svn] [Git][med-team/toil][master] add cwltool dependency

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / toil


Commits:
2120982d by Michael R. Crusoe at 2018-02-11T11:02:36-08:00
add cwltool dependency

- - - - -


1 changed file:

- debian/control


Changes:

=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -9,7 +9,8 @@ Build-Depends: debhelper (>= 10),
python-setuptools,
python-docker,
python-bd2k,
-   python-galaxy-lib
+   python-galaxy-lib,
+   cwltool
 Standards-Version: 3.9.8
 Homepage: https://github.com/BD2KGenomics/toil
 X-Python-Version: >= 2.6
@@ -20,7 +21,7 @@ Vcs-Browser: 
https://anonscm.debian.org/cgit/debian-med/toil.git
 
 Package: toil
 Architecture: all
-Depends: ${python:Depends}, ${misc:Depends}, python-cgcloud-lib
+Depends: ${python:Depends}, ${misc:Depends}, python-cgcloud-lib, cwltool
 #Suggests: python-toil-doc
 Description: cross-platform workflow engine
  Toil is a scalable, efficient, cross-platform and easy-to-use workflow



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[med-svn] [Git][med-team/cwltool] Pushed new tag upstream/1.0.20180130110340

[Michael R. Crusoe]

Michael R. Crusoe pushed new tag upstream/1.0.20180130110340 at Debian Med / 
cwltool

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[med-svn] [Git][med-team/cwltool] Pushed new tag upstream/1.0.20180211183944

[Michael R. Crusoe]

Michael R. Crusoe pushed new tag upstream/1.0.20180211183944 at Debian Med / 
cwltool

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[med-svn] [Git][med-team/jellyfish] Deleted branch me

[Michael R. Crusoe]

Michael R. Crusoe deleted branch me at Debian Med / jellyfish

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[med-svn] [Git][med-team/jellyfish][pristine-tar] pristine-tar data for jellyfish_2.2.8.orig.tar.gz

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch pristine-tar at Debian Med / jellyfish


Commits:
c1f81efb by Michael R. Crusoe at 2018-02-11T04:40:49-08:00
pristine-tar data for jellyfish_2.2.8.orig.tar.gz

- - - - -


2 changed files:

- + jellyfish_2.2.8.orig.tar.gz.delta
- + jellyfish_2.2.8.orig.tar.gz.id


Changes:

=
jellyfish_2.2.8.orig.tar.gz.delta
=
Binary files /dev/null and b/jellyfish_2.2.8.orig.tar.gz.delta differ


=
jellyfish_2.2.8.orig.tar.gz.id
=
--- /dev/null
+++ b/jellyfish_2.2.8.orig.tar.gz.id
@@ -0,0 +1 @@
+a4de0244130b8f044c031640c33c5282502612e8



View it on GitLab: 
https://salsa.debian.org/med-team/jellyfish/commit/c1f81efbd9fa080fae0cec69607316c79d776d56

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[med-svn] [Git][med-team/jellyfish] Pushed new branch me

[Michael R. Crusoe]

Michael R. Crusoe pushed new branch me at Debian Med / jellyfish

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[med-svn] [Git][med-team/jellyfish][master] 3 commits: New upstream version 2.2.8

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / jellyfish


Commits:
d2ced9a4 by Michael R. Crusoe at 2018-02-11T04:40:47-08:00
New upstream version 2.2.8
- - - - -
bd0b9735 by Michael R. Crusoe at 2018-02-11T04:40:49-08:00
Update upstream source from tag upstream/2.2.8

Update to upstream version 2.2.8
with Debian dir 7394e13779989895c917beecd9eaf77da6e91226
- - - - -
c2cdb414 by Michael R. Crusoe at 2018-02-11T09:22:01-08:00
2.2.8

- - - - -


30 changed files:

- Makefile.am
- configure.ac
- debian/changelog
- debian/control
- debian/patches/drop-rpath
- debian/patches/portability.patch
- − debian/patches/rename-python-module-to-dna_jellyfish.patch
- debian/patches/series
- + debian/patches/skip_small_mers.sh
- debian/watch
- include/jellyfish/file_header.hpp
- include/jellyfish/hash_counter.hpp
- include/jellyfish/large_hash_array.hpp
- include/jellyfish/mer_overlap_sequence_parser.hpp
- include/jellyfish/rectangular_binary_matrix.hpp
- include/jellyfish/whole_sequence_parser.hpp
- jellyfish/dbg.cc
- lib/rectangular_binary_matrix.cc
- swig/Makefile.am
- swig/jellyfish.i
- swig/python/setup.py
- swig/python/test_hash_counter.py
- swig/python/test_mer_file.py
- swig/python/test_string_mers.py
- swig/ruby/test_hash_counter.rb
- swig/ruby/test_mer_file.rb
- swig/ruby/test_string_mers.rb
- swig/string_mers.i
- tests/compat.sh.in
- unit_tests/test_file_header.cc


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/jellyfish/compare/746d4a7ebb994913da196ec16e1a885aa41c63b6...c2cdb414c927d03d225db69bacd80490554c75fb

---
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[med-svn] [Git][med-team/ncbi-blastplus] Pushed new tag debian/2.7.1-1

[Olivier Sallou]

Olivier Sallou pushed new tag debian/2.7.1-1 at Debian Med / ncbi-blastplus

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[med-svn] [Git][med-team/ncbi-blastplus][master] 2 commits: new upstream release 2.7.1

[Olivier Sallou]

Olivier Sallou pushed to branch master at Debian Med / ncbi-blastplus


Commits:
e4bfa6dd by Olivier Sallou at 2018-02-11T17:54:15+00:00
new upstream release 2.7.1

- - - - -
926ddb0d by Olivier Sallou at 2018-02-11T18:30:46+00:00
Merge branch master of salsa.debian.org:med-team/ncbi-blastplus

- - - - -


4 changed files:

- debian/changelog
- + debian/patches/fix_unit_tests
- debian/patches/series
- debian/rules


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,15 +1,10 @@
-ncbi-blast+ (2.7.1-1) UNRELEASED; urgency=medium
+ncbi-blast+ (2.7.1-1) unstable; urgency=medium
 
   * New upstream release
 d/patches: update patch for new release
 d/control:
   go to standards 4.1.3
   add mbedtls dependency
-
-
-[TODO]
-new embedded library mbedtls in c++/src/connect/
-some unit tests are failing due to symbols not found
 
  -- Olivier Sallou   Sat, 10 Feb 2018 17:35:31 +
 


=
debian/patches/fix_unit_tests
=
--- /dev/null
+++ b/debian/patches/fix_unit_tests
@@ -0,0 +1,14 @@
+Subject: add missing lib for tests
+Description: unit_test need blast lib to compile
+Forwarded: Not-Needed 
+Author: Olivier Sallou 
+Last-Updated: 2018-02-11
+--- a/c++/src/algo/blast/Makefile.blast_macros.mk
 b/c++/src/algo/blast/Makefile.blast_macros.mk
+@@ -21,5 +21,5 @@
+ BLAST_LDEP = xalgoblastdbindex composition_adjustment \
+   xalgodustmask xalgowinmask seqmasks_io seqdb blast_services 
xalnmgr \
+   xobjutil $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb 
scoremat tables
+-BLAST_LIBS = proteinkmer xblast $(BLAST_LDEP)
++BLAST_LIBS = proteinkmer xblast blast $(BLAST_LDEP)
+ # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)


=
debian/patches/series
=
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -11,3 +11,4 @@ fix_configure
 support_x32
 suppress_gnutls_version_check
 optionally_keep_sequence
+fix_unit_tests


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -125,5 +125,5 @@ override_dh_gencontrol-indep:
dh_gencontrol -Nblast2
 
 %:
-   dh $@ -Dc++ --with autotools_dev
-   #dh $@ -Dc++
+   #dh $@ -Dc++ --with autotools_dev
+   dh $@ -Dc++



View it on GitLab: 
https://salsa.debian.org/med-team/ncbi-blastplus/compare/018c8136ce2e54dd484dfe072b00aa8d1bbee0b5...926ddb0dcdd55dc46c76f94d7fe9c5a71e684946

---
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[med-svn] [Git][med-team/toil][master] 4 commits: tags are now on GitHub

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / toil


Commits:
adf12c32 by Michael R. Crusoe at 2018-02-10T04:17:32-08:00
tags are now on GitHub

- - - - -
75460763 by Michael R. Crusoe at 2018-02-10T04:18:57-08:00
New upstream version 3.14.0
- - - - -
07ff5654 by Michael R. Crusoe at 2018-02-10T04:19:05-08:00
Update upstream source from tag upstream/3.14.0

Update to upstream version 3.14.0
with Debian dir f51885e51d03d4865ae0855d2d6661f5da606493
- - - - -
1d8e7721 by Michael R. Crusoe at 2018-02-11T09:30:44-08:00
3.14.0-1

- - - - -


25 changed files:

- + .gitignore
- + .travis.yml
- + CODE_OF_CONDUCT.md
- + CONTRIBUTING.md
- + LICENSE.txt
- + Makefile
- − PKG-INFO
- README.rst
- + ROADMAP.md
- + attic/README.md
- + attic/absolute_imports.py
- + attic/jobTreeSlides.pdf
- + attic/toil-sort-example.py
- + contrib/azure/LICENSE
- + contrib/azure/README.md
- + contrib/azure/agent-0.json
- + contrib/azure/agent-gt0.json
- + contrib/azure/azuredeploy.json
- + contrib/azure/azuredeploy.parameters.json
- + contrib/azure/configure-mesos-cluster.sh
- + contrib/azure/configure-ubuntu.sh
- + contrib/azure/images/mesos.png
- + contrib/azure/jumpbox-linux.json
- + contrib/azure/jumpbox-none.json
- + contrib/azure/jumpbox-windows.json


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/toil/compare/9f00fae0b31231119692bf01ae760c663cfc66ed...1d8e7721e67424d6ac7a1ddfeede724b6b0af701

---
View it on GitLab: 
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[med-svn] [Git][med-team/toil][upstream] New upstream version 3.14.0

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch upstream at Debian Med / toil


Commits:
75460763 by Michael R. Crusoe at 2018-02-10T04:18:57-08:00
New upstream version 3.14.0
- - - - -


25 changed files:

- + .gitignore
- + .travis.yml
- + CODE_OF_CONDUCT.md
- + CONTRIBUTING.md
- + LICENSE.txt
- + Makefile
- − PKG-INFO
- README.rst
- + ROADMAP.md
- + attic/README.md
- + attic/absolute_imports.py
- + attic/jobTreeSlides.pdf
- + attic/toil-sort-example.py
- + contrib/azure/LICENSE
- + contrib/azure/README.md
- + contrib/azure/agent-0.json
- + contrib/azure/agent-gt0.json
- + contrib/azure/azuredeploy.json
- + contrib/azure/azuredeploy.parameters.json
- + contrib/azure/configure-mesos-cluster.sh
- + contrib/azure/configure-ubuntu.sh
- + contrib/azure/images/mesos.png
- + contrib/azure/jumpbox-linux.json
- + contrib/azure/jumpbox-none.json
- + contrib/azure/jumpbox-windows.json


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/toil/commit/75460763799f859d80d206cbd6a65d0425525ae9

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[med-svn] [Git][med-team/toil] Pushed new tag upstream/3.14.0

[Michael R. Crusoe]

Michael R. Crusoe pushed new tag upstream/3.14.0 at Debian Med / toil

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[med-svn] [Git][med-team/toil][pristine-tar] pristine-tar data for toil_3.14.0.orig.tar.gz

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch pristine-tar at Debian Med / toil


Commits:
b26d7204 by Michael R. Crusoe at 2018-02-10T04:19:05-08:00
pristine-tar data for toil_3.14.0.orig.tar.gz

- - - - -


2 changed files:

- + toil_3.14.0.orig.tar.gz.delta
- + toil_3.14.0.orig.tar.gz.id


Changes:

=
toil_3.14.0.orig.tar.gz.delta
=
Binary files /dev/null and b/toil_3.14.0.orig.tar.gz.delta differ


=
toil_3.14.0.orig.tar.gz.id
=
--- /dev/null
+++ b/toil_3.14.0.orig.tar.gz.id
@@ -0,0 +1 @@
+cc1bbb69a50ad3a798aec17db5d8a4a548674fde



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[med-svn] [Git][med-team/bcbio] Pushed new branch upstream

[Steffen Möller]

Steffen Möller pushed new branch upstream at Debian Med / bcbio

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[med-svn] [Git][med-team/bcbio] Pushed new branch pristine-tar

[Steffen Möller]

Steffen Möller pushed new branch pristine-tar at Debian Med / bcbio

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[med-svn] [Git][med-team/bcbio] Pushed new branch master

[Steffen Möller]

Steffen Möller pushed new branch master at Debian Med / bcbio

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[med-svn] [Git][med-team/bcbio] Pushed new tag upstream/1.0.8

[Steffen Möller]

Steffen Möller pushed new tag upstream/1.0.8 at Debian Med / bcbio

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[med-svn] [Git][med-team/porechop][master] fix dependency to seqan

[Cédric Lood]

Cédric Lood pushed to branch master at Debian Med / porechop


Commits:
0e372d3b by Cédric Lood at 2018-02-11T18:25:51+01:00
fix dependency to seqan

- - - - -


1 changed file:

- debian/control


Changes:

=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,8 @@ Maintainer: Debian Med Packaging Team 

 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10)
+Build-Depends: debhelper (>= 10),
+  libseqan2-dev
 Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/pkg-grass/porechop.git
 Vcs-Git: https://anonscm.debian.org/git/pkg-grass/porechop.git



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[med-svn] [Git][med-team/jellyfish] Pushed new tag debian/2.2.8-1

[Michael R. Crusoe]

Michael R. Crusoe pushed new tag debian/2.2.8-1 at Debian Med / jellyfish

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[med-svn] [Git][med-team/jellyfish] Pushed new tag upstream/2.2.8

[Michael R. Crusoe]

Michael R. Crusoe pushed new tag upstream/2.2.8 at Debian Med / jellyfish

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[med-svn] [Git][med-team/trinityrnaseq] Pushed new tag debian/2.2.0+dfsg-5

[Michael R. Crusoe]

Michael R. Crusoe pushed new tag debian/2.2.0+dfsg-5 at Debian Med / 
trinityrnaseq

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[med-svn] [Git][med-team/trinityrnaseq][upstream] New upstream version 2.5.1+dfsg

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch upstream at Debian Med / trinityrnaseq


Commits:
20fbb211 by Michael R. Crusoe at 2018-02-11T04:55:06-08:00
New upstream version 2.5.1+dfsg
- - - - -


21 changed files:

- .gitmodules
- + Analysis/DifferentialExpression/DTE_to_DTU.pl
- + Analysis/DifferentialExpression/GOplot.Rscript
- + Analysis/DifferentialExpression/Glimma.Trinity.Rscript
- Analysis/DifferentialExpression/PtR
- Analysis/DifferentialExpression/R/misc_rnaseq_funcs.R
- Analysis/DifferentialExpression/R/rnaseq_plot_funcs.R
- + Analysis/DifferentialExpression/R/vioplot2.R
- Analysis/DifferentialExpression/analyze_diff_expr.pl
- + Analysis/DifferentialExpression/plot_all_DE_MAplots.Rscript
- + Analysis/DifferentialExpression/plot_all_DE_volcanos.Rscript
- + Analysis/DifferentialExpression/prep_n_run_GOplot.pl
- + Analysis/DifferentialExpression/prune_isoforms_fasta.pl
- + Analysis/DifferentialExpression/prune_isoforms_gtf.pl
- Analysis/DifferentialExpression/run_DE_analysis.pl
- Analysis/DifferentialExpression/run_GOseq.pl
- + Analysis/DifferentialExpression/validate_UP_subset.Rscript
- Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
- Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl
- + Analysis/FL_reconstruction_analysis/util/blat_psl_to_align_summary_stats.pl
- + Analysis/FL_reconstruction_analysis/util/blat_query_top_hit_extractor.pl


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/trinityrnaseq/commit/20fbb21125d693fcf75d0f123f4375d7bc2a8559

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[med-svn] [Git][med-team/trinityrnaseq] Pushed new tag upstream/2.5.1+dfsg

[Michael R. Crusoe]

Michael R. Crusoe pushed new tag upstream/2.5.1+dfsg at Debian Med / 
trinityrnaseq

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[med-svn] [Git][med-team/trinityrnaseq][pristine-tar] pristine-tar data for trinityrnaseq_2.5.1+dfsg.orig.tar.xz

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch pristine-tar at Debian Med / trinityrnaseq


Commits:
e9ef5100 by Michael R. Crusoe at 2018-02-11T04:55:38-08:00
pristine-tar data for trinityrnaseq_2.5.1+dfsg.orig.tar.xz

- - - - -


2 changed files:

- + trinityrnaseq_2.5.1+dfsg.orig.tar.xz.delta
- + trinityrnaseq_2.5.1+dfsg.orig.tar.xz.id


Changes:

=
trinityrnaseq_2.5.1+dfsg.orig.tar.xz.delta
=
Binary files /dev/null and b/trinityrnaseq_2.5.1+dfsg.orig.tar.xz.delta differ


=
trinityrnaseq_2.5.1+dfsg.orig.tar.xz.id
=
--- /dev/null
+++ b/trinityrnaseq_2.5.1+dfsg.orig.tar.xz.id
@@ -0,0 +1 @@
+5f97c59fe8b890ad8dc34e8f54e8b123a10c68aa



View it on GitLab: 
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[med-svn] [Git][med-team/trinityrnaseq][master] 5 commits: fix watch

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / trinityrnaseq


Commits:
d8056e04 by Michael R. Crusoe at 2018-02-11T04:45:47-08:00
fix watch

- - - - -
20fbb211 by Michael R. Crusoe at 2018-02-11T04:55:06-08:00
New upstream version 2.5.1+dfsg
- - - - -
d5a2e951 by Michael R. Crusoe at 2018-02-11T04:55:38-08:00
Update upstream source from tag upstream/2.5.1+dfsg

Update to upstream version 2.5.1+dfsg
with Debian dir c8feebbacd500a9a363220ddc8fe113ac040322b
- - - - -
3773d9b0 by Michael R. Crusoe at 2018-02-11T05:08:05-08:00
2.5.1+dfsg

- - - - -
45363394 by Michael R. Crusoe at 2018-02-11T09:14:29-08:00
Re-add NeedlemanWunschGotohBanded  fix namespace

- - - - -


21 changed files:

- .gitmodules
- + Analysis/DifferentialExpression/DTE_to_DTU.pl
- + Analysis/DifferentialExpression/GOplot.Rscript
- + Analysis/DifferentialExpression/Glimma.Trinity.Rscript
- Analysis/DifferentialExpression/PtR
- Analysis/DifferentialExpression/R/misc_rnaseq_funcs.R
- Analysis/DifferentialExpression/R/rnaseq_plot_funcs.R
- + Analysis/DifferentialExpression/R/vioplot2.R
- Analysis/DifferentialExpression/analyze_diff_expr.pl
- + Analysis/DifferentialExpression/plot_all_DE_MAplots.Rscript
- + Analysis/DifferentialExpression/plot_all_DE_volcanos.Rscript
- + Analysis/DifferentialExpression/prep_n_run_GOplot.pl
- + Analysis/DifferentialExpression/prune_isoforms_fasta.pl
- + Analysis/DifferentialExpression/prune_isoforms_gtf.pl
- Analysis/DifferentialExpression/run_DE_analysis.pl
- Analysis/DifferentialExpression/run_GOseq.pl
- + Analysis/DifferentialExpression/validate_UP_subset.Rscript
- Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
- Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl
- + Analysis/FL_reconstruction_analysis/util/blat_psl_to_align_summary_stats.pl
- + Analysis/FL_reconstruction_analysis/util/blat_query_top_hit_extractor.pl


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/trinityrnaseq/compare/cd46bb1150f3fc470888efa37a4b37abce3719ce...45363394b4b284c0cb9012dc5bb10aa36d9bf1a6

---
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[med-svn] [Git][med-team/porechop][master] 2 commits: Remove template boilerplate

[Cédric Lood]

Cédric Lood pushed to branch master at Debian Med / porechop


Commits:
00ae04d3 by Andreas Tille at 2018-02-11T18:12:07+01:00
Remove template boilerplate

- - - - -
e200c033 by Andreas Tille at 2018-02-11T18:13:03+01:00
Cleanup rules file

- - - - -


2 changed files:

- − debian/get-orig-source
- debian/rules


Changes:

=
debian/get-orig-source deleted
=
--- a/debian/get-orig-source
+++ /dev/null
@@ -1,45 +0,0 @@
-#!/bin/sh
-# if you need to repack for whatever reason you can
-# use this script via uscan or directly
-#
-# FIXME: currently the code is not conform to Debian Policy
-#http://www.debian.org/doc/debian-policy/ch-source.html
-#"get-orig-source (optional)"
-#This target may be invoked in any directory, ...
-# --> currently it is assumed the script is called in the
-# source directory featuring the debian/ dir
-
-COMPRESS=xz
-
-set -e
-NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
-
-if ! echo $@ | grep -q upstream-version ; then
-VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 
's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
-uscan --force-download
-else
-VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) 
.*${NAME}.*?\1?"`
-if echo "$VERSION" | grep -q "upstream-version" ; then
-echo "Unable to parse version number"
-exit
-fi
-fi
-
-TARDIR=${NAME}-${VERSION}
-mkdir -p ../tarballs
-cd ../tarballs
-# need to clean up the tarballs dir first because upstream tarball might
-# contain a directory with unpredictable name
-rm -rf *
-tar -xaf ../${TARDIR}.tar.gz
-
-UPSTREAMTARDIR=`find . -mindepth 1 -maxdepth 1 -type d`
-if [ "${UPSTREAMTARDIR}" != "${TARDIR}" ] ; then
-mv "${UPSTREAMTARDIR}" "${TARDIR}"
-fi
-
-# Remove useless binaries
-# ... do something which needs to be done ...
-
-GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX -caf 
"$NAME"_"$VERSION".orig.tar.${COMPRESS} "${TARDIR}"
-rm -rf ${TARDIR}


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -1,24 +1,6 @@
 #!/usr/bin/make -f
 
 # DH_VERBOSE := 1
-export LC_ALL=C.UTF-8
-
-# some helpful variables - uncomment them if needed
-# shamelessly stolen from http://jmtd.net/log/awk/
-#DEBVERS:= $(shell dpkg-parsechangelog | awk '/^Version:/ {print $$2}')
-#VERSION:= $(shell echo '$(DEBVERS)' | sed -e 's/^[0-9]*://' -e 
's/-.*//')
-#DEBFLAVOR  := $(shell dpkg-parsechangelog | awk '/^Distribution:/ {print 
$$2}')
-#DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
-#DEBIAN_BRANCH  := $(shell awk 'BEGIN{FS="[= ]+"} /debian-branch/ {print $$2}' 
debian/gbp.conf)
-#GIT_TAG:= $(subst ~,_,$(VERSION))
-
-# alternatively to manually set those variables you can
-#  include /usr/share/cdbs/1/rules/buildvars.mk
-# and use what is set there.  Any hint whether dh might set variables in
-# a similar manner are welcome.
 
 %:
-   dh $@ --parallel
-
-#get-orig-source:
-#  . debian/get-orig-source
+   dh $@



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---
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[med-svn] [Git][med-team/mhap][master] 2 commits: Fix yaml syntax

[Sascha Steinbiss]

Sascha Steinbiss pushed to branch master at Debian Med / mhap


Commits:
3110815f by Andreas Tille at 2017-08-17T19:16:43+02:00
Fix yaml syntax

- - - - -
1cb04d5d by Andreas Tille at 2017-10-20T10:09:25+02:00
Fix OMICS entry

- - - - -


1 changed file:

- debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -10,5 +10,5 @@ Reference:
   PMID: 26006009
   URL: http://www.nature.com/nbt/journal/v33/n6/full/nbt.3238.html
 Registry:
-  -Name: OMICtools
-   Entry: OMIC_13515
+  - Name: OMICtools
+Entry: OMICS_13515



View it on GitLab: 
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---
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[med-svn] [Debian Wiki] Update of "DebianMed/SoftwareLiberation" by AndreasTille

[Debian Wiki]

Dear Wiki user,

You have subscribed to a wiki page or wiki category on "Debian Wiki" for change 
notification.

The "DebianMed/SoftwareLiberation" page has been changed by AndreasTille:
https://wiki.debian.org/DebianMed/SoftwareLiberation?action=diff=46=47

Comment:
emmax

  ||[[https://github.com/chairmank/locfit|locfit]]  
||[[https://github.com/chairmank/locfit/issues/1|Issue on Github]] ||No answer 
yet||2017-09-06||
  ||[[https://github.com/rambaut/Seq-Gen|seq-gen]]  
||[[https://github.com/rambaut/Seq-Gen/issues/10|Issue on Github]] ||No answer 
yet||2017-09-06||
  ||[[http://www.bork.embl.de/pal2nal|pal2nal]] 
||[[https://lists.debian.org/debian-med/2017/10/msg00019.html|Debian Med list]] 
||[[https://lists.debian.org/debian-med/2017/10/msg00024.html|Author will 
change to GPL]]||2017-10-10||
+ ||[[https://genome.sph.umich.edu/wiki/EMMAX|emmax]]   
||[[https://lists.debian.org/debian-med/2018/02/msg00023.html|Debian Med 
list]]||No answer yet||2018-02-11||
  
  == Known, but not pursued ==
  ||'''Software'''  
||'''Reason'''||

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[med-svn] [Debian Wiki] Update of "DebianMed/SoftwareLiberation" by AndreasTille

[Debian Wiki]

Dear Wiki user,

You have subscribed to a wiki page or wiki category on "Debian Wiki" for change 
notification.

The "DebianMed/SoftwareLiberation" page has been changed by AndreasTille:
https://wiki.debian.org/DebianMed/SoftwareLiberation?action=diff=45=46

Comment:
ffp

  
||[[http://molevol.cmima.csic.es/castresana/Gblocks.html|gblocks]]||[[https://lists.debian.org/debian-med/2011/02/msg8.html|Debian
 Med list]] ||No answer yet||2011-02-02||
  ||[[http://genome.ucsc.edu/cgi-bin/hgBlat|blat]]  
||[[https://lists.alioth.debian.org/pipermail/debian-med-packaging/2014-March/025516.html|Debian
 Med packaging 
list]]||[[https://lists.alioth.debian.org/pipermail/debian-med-packaging/2015-December/037177.html|Further
 discussion]]||2015-12-11||
  ||[[http://varscan.sourceforge.net/|varscan]] 
||[[https://github.com/dkoboldt/varscan/issues/12|Issue on 
Github]]||[[https://github.com/dkoboldt/varscan/issues/12|Issue closed]]|| 
2016-11-01 ||
- ||[[http://sourceforge.net/projects/ffp-phylogeny|ffp]]   
||[[https://lists.debian.org/debian-med/2015/11/msg00058.html|Debian Med 
list]]|| No answer yet || 2015-11-26 ||
+ ||[[http://sourceforge.net/projects/ffp-phylogeny|ffp]]   
||[[https://lists.debian.org/debian-med/2015/11/msg00058.html|Debian Med 
list]]|| [[https://lists.debian.org/debian-med/2018/02/msg6.html|Redirected 
question to responsible person]] || 2015-11-26 ||
  
||[[https://www-gene.cimr.cam.ac.uk/MSgenetics/GAMES/MSSS/|mssstest]]||[[https://lists.debian.org/debian-med/2016/01/msg00055.html|Debian
 Med 
list]]||[[https://lists.debian.org/debian-med/2016/01/msg00084.html|Refused]]||2016-01-15||
  ||[[http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/|cluster3]] 
||[[https://lists.debian.org/debian-med/2016/01/msg00194.html|Debian Med list]] 
||[[https://lists.debian.org/debian-med/2016/02/msg0.html|Michiel de Hoon]] 
|| 2016-02-01||
  ||[[http://sift.jcvi.org/|blimps and sift]]   
||[[https://lists.debian.org/debian-med/2016/01/msg00056.html|Debian Med list]] 
||[[https://lists.debian.org/debian-med/2016/01/msg00085.html|Pauline Ng]]: 
Dual license GPL possible || 2016-01-15 ||

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