[med-svn] [Git][med-team/libbpp-core][master] 2 commits: Fixed copyright file.

2018-04-06 Thread Julien Y. Dutheil 
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-core


Commits:
07f15714 by Julien Y. Dutheil at 2018-04-07T07:31:20+02:00
Fixed copyright file.

- - - - -
cc18852b by Julien Y. Dutheil at 2018-04-07T07:31:34+02:00
Merge branch master of ssh://salsa.debian.org/med-team/libbpp-core

- - - - -


1 changed file:

- debian/copyright


Changes:

=
debian/copyright
=
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,11 +1,11 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: B++-Core
+Upstream-Name: Bpp-Core
 Upstream-Contact: Julien Yann Dutheil 
-Source: http://biopp.univ-montp2.fr/Repositories/sources/
+Source: https://github.com/BioPP/bpp-core/
 
 Files: *
 Copyright: 2010-2016 Julien Yann Dutheil 
-   Bio++ Development Team
+ Bio++ Development Team
 License: CeCILL
 
 Files: debian/*



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[med-svn] [Git][med-team/spread-phy] Pushed new branch debian/jessie-backports

2018-04-06 Thread Andreas Tille 
Andreas Tille pushed new branch debian/jessie-backports at Debian Med / 
spread-phy

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[med-svn] [Git][med-team/spread-phy][master] 4 commits: Standards-Version: 4.1.4

2018-04-06 Thread Andreas Tille 
Andreas Tille pushed to branch master at Debian Med / spread-phy


Commits:
7ea3935b by Andreas Tille at 2018-04-06T23:30:52+02:00
Standards-Version: 4.1.4

- - - - -
d50480b5 by Andreas Tille at 2018-04-06T23:31:03+02:00
Point Vcs fields to salsa.debian.org

- - - - -
f4043284 by Andreas Tille at 2018-04-06T23:31:23+02:00
debhelper 11

- - - - -
252db77d by Andreas Tille at 2018-04-07T07:13:52+02:00
Upload to unstable

- - - - -


3 changed files:

- debian/changelog
- debian/compat
- debian/control


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,11 +1,14 @@
-spread-phy (1.0.7+dfsg-2) UNRELEASED; urgency=medium
+spread-phy (1.0.7+dfsg-2) unstable; urgency=medium
 
   * cme fix dpkg-control
   * d/watch:
  - version=4
  - xz compression
+  * Standards-Version: 4.1.4
+  * Point Vcs fields to salsa.debian.org
+  * debhelper 11
 
- -- Andreas Tille   Tue, 03 Jan 2017 09:03:13 +0100
+ -- Andreas Tille   Fri, 06 Apr 2018 23:31:27 +0200
 
 spread-phy (1.0.7+dfsg-1) unstable; urgency=medium
 


=
debian/compat
=
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-10
+11


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

 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
javahelper,
ant,
ant-optional,
@@ -12,9 +12,9 @@ Build-Depends: debhelper (>= 10),
libcolt-free-java,
libprocessing-core-java,
libfest-assert-java
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/spread-phy.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/spread-phy.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/spread-phy
+Vcs-Git: https://salsa.debian.org/med-team/spread-phy.git
 Homepage: http://www.kuleuven.be/aidslab/phylogeography/SPREAD.html
 
 Package: spread-phy



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[med-svn] [Git][med-team/spread-phy] Pushed new tag debian/1.0.7+dfsg-2

2018-04-06 Thread Andreas Tille 
Andreas Tille pushed new tag debian/1.0.7+dfsg-2 at Debian Med / spread-phy

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[med-svn] [Git][med-team/srst2][master] Updated RRID in d/u/metadata

2018-04-06 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / srst2


Commits:
b453e908 by Steffen Möller at 2018-04-06T12:06:07+00:00
Updated RRID in d/u/metadata
- - - - -


1 changed file:

- debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -1,12 +1,24 @@
 Reference:
-  Author: Michael Inouye and Harriet Dashnow and Lesley-Ann Raven and Mark B 
Schultz and Bernard J Pope and Takehiro Tomita and Justin Zobel and Kathryn E 
Holt3
-  Title: "SRST2: Rapid genomic surveillance for public health and hospital 
microbiology labs"
-  Journal: Genome Medicine
-  Year:  2014
-  Volume: 6
-  Number: 11
-  Pages: 90
-  DOI: 10.1186/s13073-014-0090-6
-  PMID: 25422674
-  URL: http://www.genomemedicine.com/content/6/11/90
-  eprint: http://www.genomemedicine.com/content/pdf/s13073-014-0090-6.pdf
+ Author: >
+  Michael Inouye and Harriet Dashnow and Lesley-Ann Raven and
+  Mark B Schultz and Bernard J Pope and Takehiro Tomita and Justin Zobel and
+  Kathryn E Holt
+ Title: >
+  SRST2: Rapid genomic surveillance for public health and
+  hospital microbiology labs
+ Journal: Genome Medicine
+ Year:  2014
+ Volume: 6
+ Number: 11
+ Pages: 90
+ DOI: 10.1186/s13073-014-0090-6
+ PMID: 25422674
+ URL: http://www.genomemedicine.com/content/6/11/90
+ eprint: http://www.genomemedicine.com/content/pdf/s13073-014-0090-6.pdf
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_12777
+ - Name: bio.tools
+   Entry: NA
+ - Name: SciCrunch
+   Entry: NA
\ No newline at end of file



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[med-svn] [Git][med-team/transdecoder][master] Added new d/u/metadata file.

2018-04-06 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / transdecoder


Commits:
786e4524 by Steffen Möller at 2018-04-06T12:15:43+00:00
Added new d/u/metadata file.

RRID only.
- - - - -


1 changed file:

- + debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,7 @@
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_10852
+ - Name: SciCrunch
+   Entry: NA
+ - Name: bio.tools
+   Entry: NA



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[med-svn] [Git][med-team/sra-sdk][master] Updated OMICtools RRID in d/u/metadata

2018-04-06 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / sra-sdk


Commits:
b2cfa436 by Steffen Möller at 2018-04-06T12:03:12+00:00
Updated OMICtools RRID in d/u/metadata
- - - - -


1 changed file:

- debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -26,4 +26,4 @@ Registry:
   - Name: RRID
 Entry: NA
   - Name: OMICtools
-Entry: NA
+Entry: OMICS_03771



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[med-svn] [Git][med-team/theseus][master] Updated RRID in d/u/metadata

2018-04-06 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / theseus


Commits:
8081a5e4 by Steffen Möller at 2018-04-06T12:12:22+00:00
Updated RRID in d/u/metadata
- - - - -


1 changed file:

- debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -1,17 +1,23 @@
 Name: Theseus
 Reference:
  - Author: Theobald, Douglas L. and Wuttke, Deborah S.
-   Title: "THESEUS: maximum likelihood superpositioning and analysis of 
macromolecular structures"
+   Title: 
+THESEUS: maximum likelihood superpositioning and analysis of
+macromolecular structures
Journal: Bioinformatics
Volume: 22
Number: 17
Pages: 2171-2172
DOI: 10.1093/bioinformatics/btl332
Year: 2006
-   URL: 
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/17/2171
-   eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/22/17/2171.pdf
+   URL: >
+http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/17/2171
+   eprint: >
+http://bioinformatics.oxfordjournals.org/cgi/reprint/22/17/2171.pdf
  - Author: Theobald, Douglas L. and Wuttke, Deborah S.
-   Title: Empirical Bayes hierarchical models for regularizing maximum 
likelihood estimation in the matrix Gaussian Procrustes problem
+   Title: >
+Empirical Bayes hierarchical models for regularizing maximum likelihood
+estimation in the matrix Gaussian Procrustes problem
Journal: Proceedings of the National Academy of Sciences
Volume: 103
Number: 49
@@ -21,7 +27,8 @@ Reference:
URL: http://www.pnas.org/content/103/49/18521.abstract
eprint: http://www.pnas.org/content/103/49/18521.full.pdf+html
  - Author: Theobald, Douglas L. and Wuttke, Deborah S.
-   Title: Accurate Structural Correlations from Maximum Likelihood 
Superpositions
+   Title: >
+Accurate Structural Correlations from Maximum Likelihood Superpositions
Journal: PLoS Comput Biol
Publisher: Public Library of Science
Year: 2008
@@ -31,3 +38,10 @@ Reference:
Pages: e43
Number: 2
DOI: 10.1371/journal.pcbi.0040043
+Registry:
+ - Name: OMICtools
+   Entry: Theseus
+ - Name: bio.tools
+   Entry: NA
+ - Name: SciCrunch
+   Entry: NA



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[med-svn] [Git][med-team/tree-puzzle][master] Updated RRID in d/u/metadata

2018-04-06 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / tree-puzzle


Commits:
1ef53aaf by Steffen Möller at 2018-04-06T12:20:29+00:00
Updated RRID in d/u/metadata
- - - - -


1 changed file:

- debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -61,3 +61,11 @@ Reference:
URL: http://www.sciencedirect.com/science/article/pii/S0743731503001291
eprint: 
http://pdn.sciencedirect.com/science?_ob=MiamiImageURL&_cid=272438&_user=661252&_pii=S0743731503001291&_check=y&_origin=article&_zone=toolbar&_coverDate=31-Aug-2003=c=serial=dGLbVlt-zSkWb=3ed4a64214b45f1cd935565b0cbc909b/1-s2.0-S0743731503001291-main.pdf
debian-package: tree-ppuzzle 
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_18458
+   debian-package: tree-puzzle
+ - Name: SciCrunch
+   Entry: NA
+ - Name: bio.tools
+   Entry: TREE-PUZZLE
\ No newline at end of file



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[med-svn] [Git][med-team/smalt][master] Add new d/u/metadata file

2018-04-06 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / smalt


Commits:
fcfc1eaf by Steffen Möller at 2018-04-06T10:38:00+00:00
Add new d/u/metadata file

RRID only.
- - - - -


1 changed file:

- + debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,7 @@
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_00686
+ - Name: SciCrunch
+   Entry: SCR_000544
+ - Name: bio.tools
+   Entry: Smalt



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[med-svn] [Git][med-team/smrtanalysis][master] Added new d/u/metadata file

2018-04-06 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / smrtanalysis


Commits:
75c7bc04 by Steffen Möller at 2018-04-06T10:44:14+00:00
Added new d/u/metadata file

RRID only
- - - - -


1 changed file:

- + debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,8 @@
+Name: SMRT Analysis
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_05142
+ - Name: SciCrunch
+   Entry: SCR_002942
+ - Name: bio.tools
+   Entry: SMRT_Analysis



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[med-svn] [Git][med-team/sprai][master] Added new d/u/metadata file

2018-04-06 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / sprai


Commits:
0f1bf61d by Steffen Möller at 2018-04-06T11:55:53+00:00
Added new d/u/metadata file

RRID only.
- - - - -


1 changed file:

- + debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,7 @@
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_21293
+ - Name: bio.tools
+   Entry: NA
+ - Name: SciCrunch
+   Entry: NA



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[med-svn] [Git][med-team/beast2-mcmc][master] s/antlr-runtime.jar/antlr4-runtime.jar/

2018-04-06 Thread Andreas Tille 
Andreas Tille pushed to branch master at Debian Med / beast2-mcmc


Commits:
e27a222f by Andreas Tille at 2018-04-06T13:43:35+02:00
s/antlr-runtime.jar/antlr4-runtime.jar/

- - - - -


1 changed file:

- debian/patches/fix_classpath_in_build_xml.patch


Changes:

=
debian/patches/fix_classpath_in_build_xml.patch
=
--- a/debian/patches/fix_classpath_in_build_xml.patch
+++ b/debian/patches/fix_classpath_in_build_xml.patch
@@ -32,7 +32,7 @@ Forwarded: no
 -
 -
 +
-+
++

[med-svn] [Git][med-team/beast2-mcmc][master] d/rules: Add antlr4-runtime.jar to CLASS_PATH

2018-04-06 Thread Andreas Tille 
Andreas Tille pushed to branch master at Debian Med / beast2-mcmc


Commits:
e424c7f2 by Andreas Tille at 2018-04-06T11:56:58+02:00
d/rules: Add antlr4-runtime.jar to CLASS_PATH

- - - - -


2 changed files:

- debian/changelog
- debian/rules


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -13,6 +13,7 @@ beast2-mcmc (2.4.8+dfsg-1) UNRELEASED; urgency=medium
   * Build-Depends: s/openjdk-8-jdk/default-jdk/
 Closes: #894359
   * Depends: s/openjdk-8-jre | java8-runtime/default-jre | java9-runtime/
+  * d/rules: Add antlr4-runtime.jar to CLASS_PATH
 
  -- Andreas Tille   Fri, 06 Apr 2018 09:03:13 +0200
 


=
debian/rules
=
--- a/debian/rules
+++ b/debian/rules
@@ -11,7 +11,7 @@ PACKAGE := $(shell dpkg-parsechangelog | sed -n 's/^Source: 
//p')
 JAVA_HOME  := /usr/lib/jvm/default-java
 
 DEBJAR:= /usr/share/java
-CLASS_PATH := 
/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:$(JAVA_HOME)/lib/tools.jar:$(DEBJAR)/beagle.jar:$(DEBJAR)/mpj.jar:$(DEBJAR)/org.boehn.kmlframework.jar:$(DEBJAR)/itext1-1.4.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:$(DEBJAR)/options.jar:$(DEBJAR)/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar
+CLASS_PATH := 
/usr/share/ant/lib/ant.jar:/usr/share/ant/lib/ant-launcher.jar:/usr/share/ant/lib/ant-nodeps.jar:/usr/share/ant/lib/ant-junit.jar:$(DEBJAR)/antlr4-runtime.jar:$(JAVA_HOME)/lib/tools.jar:$(DEBJAR)/beagle.jar:$(DEBJAR)/mpj.jar:$(DEBJAR)/org.boehn.kmlframework.jar:$(DEBJAR)/itext1-1.4.jar:$(DEBJAR)/junit4.jar:$(DEBJAR)/figtree.jar:lib/colt.jar:$(DEBJAR)/options.jar:$(DEBJAR)/mtj.jar:$(DEBJAR)/jam.jar:$(DEBJAR)/jdom1.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/commons-math.jar:/usr/lib/R/site-library/rJava/jri/JRI.jar
 
 # to run the test suite
 JAVA   := $(JAVA_HOME)/bin/java



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[med-svn] [Git][med-team/snp-sites][master] Updated OMICtools RRID in d/u/metadata

2018-04-06 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / snp-sites


Commits:
ea4e0c15 by Steffen Möller at 2018-04-06T11:35:46+00:00
Updated OMICtools RRID in d/u/metadata

And worked towards yamllint cleanliness.
- - - - -


1 changed file:

- debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -1,16 +1,22 @@
 Reference:
-  Author: Andrew J. Page and Ben Taylor and Aidan J. Delaney and Jorge Soares 
and Torsten Seemann and Jacqueline A. Keane and Simon R. Harris
-  Title: "SNP-sites: rapid efficient extraction of SNPs from multi-FASTA 
alignments"
-  Journal: Microbial Genomics
-  Year: 2016
-  Volume: 2
-  Number: 4
-  DOI: 10.1099/mgen.0.56
-  URL: 
http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.56
-  eprint: 
http://mgen.microbiologyresearch.org/deliver/fulltext/mgen/2/4/mgen56.pdf?itemId=/content/journal/mgen/10.1099/mgen.0.56=pdf=
+ Author: >
+  Andrew J. Page and Ben Taylor and Aidan J. Delaney and Jorge Soares and
+  Torsten Seemann and Jacqueline A. Keane and Simon R. Harris
+ Title: >
+  SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments
+ Journal: Microbial Genomics
+ Year: 2016
+ Volume: 2
+ Number: 4
+ DOI: 10.1099/mgen.0.56
+ URL: "http://mgen.microbiologyresearch.org/content/\
+  journal/mgen/10.1099/mgen.0.56"
+ ePrint: "http://mgen.microbiologyresearch.org/deliver/fulltext/mgen/2/4/\
+  mgen56.pdf?itemId=/content/journal/mgen/10.1099/mgen.0.56&\
+  mimeType=pdf="
 Registry:
   - Name: OMICtools
-Entry: NA
+Entry: OMICS_24972
   - Name: bio.tools
 Entry: NA
   - Name: RRID



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[med-svn] [Git][med-team/spaced][master] Updated RRID in d/u/metadata

2018-04-06 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / spaced


Commits:
745938ee by Steffen Möller at 2018-04-06T11:53:22+00:00
Updated RRID in d/u/metadata
- - - - -


1 changed file:

- debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -1,12 +1,24 @@
 Reference:
-  Author: Burkhard Morgenstern and Bingyao Zhu and Sebastian Horwege and 
Chris-Andre Leimeister
-  Title: Estimating evolutionary distances between genomic sequences from 
spaced-words matches
-  Journal: Algorithms for Molecular Biology
-  Year: 2015
-  Volume: 10
-  Number: 1
-  Pages: 1-12
-  DOI: 10.1186/s13015-015-0032-x
-  PMID: 25685176
-  URL: http://dx.doi.org/10.1186/s13015-015-0032-x
-  eprint: 
http://almob.biomedcentral.com/track/pdf/10.1186/s13015-015-0032-x?site=almob.biomedcentral.com
+ Author: >
+  Burkhard Morgenstern and Bingyao Zhu and Sebastian Horwege and
+  Chris-Andre Leimeister
+ Title: >
+  Estimating evolutionary distances between genomic sequences from
+  spaced-words matches
+ Journal: Algorithms for Molecular Biology
+ Year: 2015
+ Volume: 10
+ Number: 1
+ Pages: 1-12
+ DOI: 10.1186/s13015-015-0032-x
+ PMID: 25685176
+ URL: http://dx.doi.org/10.1186/s13015-015-0032-x
+ ePrint: "http://almob.biomedcentral.com/track/pdf/\
+  10.1186/s13015-015-0032-x?site=almob.biomedcentral.com"
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_05427
+ - Name: SciCrunch
+   Entry: NA
+ - Name: bio.tools
+   Entry: NA



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[med-svn] [Git][med-team/beast2-mcmc] Pushed new tag debian/2.4.4+dfsg-1

2018-04-06 Thread Andreas Tille 
Andreas Tille pushed new tag debian/2.4.4+dfsg-1 at Debian Med / beast2-mcmc

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[med-svn] [Git][med-team/beast2-mcmc][master] 7 commits: New upstream version 2.4.8+dfsg

2018-04-06 Thread Andreas Tille 
Andreas Tille pushed to branch master at Debian Med / beast2-mcmc


Commits:
4a8dd9ec by Andreas Tille at 2018-04-06T08:30:49+02:00
New upstream version 2.4.8+dfsg
- - - - -
4fb2c4d4 by Andreas Tille at 2018-04-06T08:31:07+02:00
Update upstream source from tag upstream/2.4.8+dfsg

Update to upstream version 2.4.8+dfsg
with Debian dir 86b98717ad86bb43bbe32a3597a184a64eaf5b2d
- - - - -
1f82c40f by Andreas Tille at 2018-04-06T09:03:53+02:00
New upstream version

- - - - -
01448b7c by Andreas Tille at 2018-04-06T09:06:53+02:00
Adapt patches

- - - - -
c1df568c by Andreas Tille at 2018-04-06T09:08:27+02:00
Point Vcs fields to salsa.debian.org

- - - - -
c254b965 by Andreas Tille at 2018-04-06T09:08:42+02:00
debhelper 11

- - - - -
06fbd6cb by Andreas Tille at 2018-04-06T09:11:31+02:00
Build-Depends: s/openjdk-8-jdk/default-jdk/

- - - - -


30 changed files:

- + .gitignore
- + .travis.yml
- + Dockerfile
- README.md
- build.xml
- debian/changelog
- debian/compat
- debian/control
- debian/patches/fix_classpath_in_build_xml.patch
- + examples/nexus/maddison.nex
- + examples/testDirectSimulator.xml
- + examples/testDirectSimulator2.xml
- + examples/testDirectSimulatorHierarchical.xml
- release/Linux/bin/addonmanager
- release/Linux/bin/appstore
- release/Linux/bin/beast
- release/Linux/bin/beauti
- release/Linux/bin/densitree
- release/Linux/bin/loganalyser
- release/Linux/bin/logcombiner
- release/Linux/bin/treeannotator
- release/Windows/AppStore_launch4j.xml
- release/Windows/BEAST_launch4j.xml
- release/Windows/BEAUti_launch4j.xml
- release/Windows/LogCombiner_launch4j.xml
- release/Windows/TreeAnnotator_launch4j.xml
- release/common/README.txt
- release/common/VERSION HISTORY.txt
- release/common/tools/DensiTree_launch4j.xml
- src/beast/app/BEASTVersion.java


The diff was not included because it is too large.


View it on GitLab: 
https://salsa.debian.org/med-team/beast2-mcmc/compare/569e2c71a54571deba0285769350bf2c6a1542f6...06fbd6cb2af7bd4c273ae5d8ab08024e91a3817c

---
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[med-svn] [Git][med-team/beast2-mcmc][upstream] New upstream version 2.4.8+dfsg

2018-04-06 Thread Andreas Tille 
Andreas Tille pushed to branch upstream at Debian Med / beast2-mcmc


Commits:
4a8dd9ec by Andreas Tille at 2018-04-06T08:30:49+02:00
New upstream version 2.4.8+dfsg
- - - - -


30 changed files:

- + .gitignore
- + .travis.yml
- + Dockerfile
- README.md
- build.xml
- + examples/nexus/maddison.nex
- + examples/testDirectSimulator.xml
- + examples/testDirectSimulator2.xml
- + examples/testDirectSimulatorHierarchical.xml
- release/Linux/bin/addonmanager
- release/Linux/bin/appstore
- release/Linux/bin/beast
- release/Linux/bin/beauti
- release/Linux/bin/densitree
- release/Linux/bin/loganalyser
- release/Linux/bin/logcombiner
- release/Linux/bin/treeannotator
- release/Windows/AppStore_launch4j.xml
- release/Windows/BEAST_launch4j.xml
- release/Windows/BEAUti_launch4j.xml
- release/Windows/LogCombiner_launch4j.xml
- release/Windows/TreeAnnotator_launch4j.xml
- release/common/README.txt
- release/common/VERSION HISTORY.txt
- release/common/tools/DensiTree_launch4j.xml
- src/beast/app/BEASTVersion.java
- src/beast/app/BEASTVersion2.java
- src/beast/app/BeastMCMC.java
- src/beast/app/beastapp/BeastDialog.java
- src/beast/app/beastapp/BeastLauncher.java


The diff was not included because it is too large.


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[med-svn] [Git][med-team/beast2-mcmc] Pushed new branch debian/jessie-backports

2018-04-06 Thread Andreas Tille 
Andreas Tille pushed new branch debian/jessie-backports at Debian Med / 
beast2-mcmc

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[med-svn] [Git][med-team/beast2-mcmc][pristine-tar] pristine-tar data for beast2-mcmc_2.4.8+dfsg.orig.tar.xz

2018-04-06 Thread Andreas Tille 
Andreas Tille pushed to branch pristine-tar at Debian Med / beast2-mcmc


Commits:
7ab38dd5 by Andreas Tille at 2018-04-06T08:31:07+02:00
pristine-tar data for beast2-mcmc_2.4.8+dfsg.orig.tar.xz

- - - - -


2 changed files:

- + beast2-mcmc_2.4.8+dfsg.orig.tar.xz.delta
- + beast2-mcmc_2.4.8+dfsg.orig.tar.xz.id


Changes:

=
beast2-mcmc_2.4.8+dfsg.orig.tar.xz.delta
=
Binary files /dev/null and b/beast2-mcmc_2.4.8+dfsg.orig.tar.xz.delta differ


=
beast2-mcmc_2.4.8+dfsg.orig.tar.xz.id
=
--- /dev/null
+++ b/beast2-mcmc_2.4.8+dfsg.orig.tar.xz.id
@@ -0,0 +1 @@
+b54bd5ea1dcdff54f916fc93568272b5b2fd68cf



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[med-svn] [Git][med-team/beast2-mcmc] Pushed new tag upstream/2.4.4+dfsg

2018-04-06 Thread Andreas Tille 
Andreas Tille pushed new tag upstream/2.4.4+dfsg at Debian Med / beast2-mcmc

---
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[med-svn] [Git][med-team/beast2-mcmc] Pushed new tag upstream/2.4.8+dfsg

2018-04-06 Thread Andreas Tille 
Andreas Tille pushed new tag upstream/2.4.8+dfsg at Debian Med / beast2-mcmc

---
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[med-svn] [Git][med-team/gmap][master] Update metadata

2018-04-06 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / gmap


Commits:
d575e778 by Steffen Möller at 2018-04-06T14:04:47+00:00
Update metadata
- - - - -


1 changed file:

- debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -17,5 +17,5 @@ Registry:
Entry: OMICS_15072
  - Name: bio.tools
Entry: gmap
- - Name: RRID
+ - Name: SciCrunch
Entry: SCR_008992



View it on GitLab: 
https://salsa.debian.org/med-team/gmap/commit/d575e778e1214e5695df380cd78323981c425c5c

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[med-svn] [Git][med-team/gmap][master] Updated bio.tools RRID in d/u/metadata

2018-04-06 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / gmap


Commits:
9472022b by Steffen Möller at 2018-04-06T14:04:31+00:00
Updated bio.tools RRID in d/u/metadata

also working towards yamllint cleanliness
- - - - -


1 changed file:

- debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -1,19 +1,21 @@
 Name: GMAP
 Reference:
-  Title: "GMAP: a genomic mapping and alignment program for mRNA and EST 
sequences"
-  Author: Thomas D. Wu, Colin K. Watanabe
-  Journal: Bioinformatics
-  Year: 2005
-  Volume: 21
-  Number: 9
-  Pages: 1859-1875
-  DOI: 10.1093/bioinformatics/bti310
-  URL: http://bioinformatics.oxfordjournals.org/content/21/9/1859.abstract
-  eprint: 
http://bioinformatics.oxfordjournals.org/content/21/9/1859.full.pdf+html
+ Title: >
+  GMAP: a genomic mapping and alignment program for mRNA and EST sequences
+ Author: Thomas D. Wu and Colin K. Watanabe
+ Journal: Bioinformatics
+ Year: 2005
+ Volume: 21
+ Number: 9
+ Pages: 1859-1875
+ DOI: 10.1093/bioinformatics/bti310
+ URL: http://bioinformatics.oxfordjournals.org/content/21/9/1859.abstract
+ ePrint: >
+  http://bioinformatics.oxfordjournals.org/content/21/9/1859.full.pdf+html
 Registry:
-  - Name: OMICtools
-Entry: OMICS_15072
-  - Name: bio.tools
-Entry: NA
-  - Name: RRID
-Entry: SCR_008992
+ - Name: OMICtools
+   Entry: OMICS_15072
+ - Name: bio.tools
+   Entry: gmap
+ - Name: RRID
+   Entry: SCR_008992



View it on GitLab: 
https://salsa.debian.org/med-team/gmap/commit/9472022b6128f563a35ec81948972dc005512e7a

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[med-svn] [Git][med-team/picard-tools][master] 5 commits: Fixed the build failure with Java 9 (Closes: #894329)

2018-04-06 Thread Emmanuel Bourg 
Emmanuel Bourg pushed to branch master at Debian Med / picard-tools


Commits:
d3eb9023 by Emmanuel Bourg at 2018-04-06T12:13:51+02:00
Fixed the build failure with Java 9 (Closes: #894329)

- - - - -
dd4c4b64 by Emmanuel Bourg at 2018-04-06T12:14:05+02:00
Standards-Version updated to 4.1.4

- - - - -
12315b01 by Emmanuel Bourg at 2018-04-06T12:14:09+02:00
Switch to debhelper level 11

- - - - -
f9300c67 by Emmanuel Bourg at 2018-04-06T17:32:05+02:00
Use salsa.debian.org Vcs-* URLs

- - - - -
e77131a1 by Emmanuel Bourg at 2018-04-06T17:36:14+02:00
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/compat
- debian/control
- debian/patches/10-build.xml.patch
- debian/patches/40-tests-fix-testng.patch


Changes:

=
debian/changelog
=
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,13 @@
+picard-tools (2.8.1+dfsg-4) unstable; urgency=medium
+
+  * Team upload.
+  * Fixed the build failure with Java 9 (Closes: #894329)
+  * Standards-Version updated to 4.1.4
+  * Switch to debhelper level 11
+  * Use salsa.debian.org Vcs-* URLs
+
+ -- Emmanuel Bourg   Fri, 06 Apr 2018 17:36:09 +0200
+
 picard-tools (2.8.1+dfsg-3) unstable; urgency=medium
 
   * debian/upstream/metadata: RRID -> SciCrunch


=
debian/compat
=
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-10
+11


=
debian/control
=
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,7 @@ Uploaders: Charles Plessy ,
 Section: science
 Priority: optional
 Build-Depends: default-jdk (>= 2:1.8),
-   debhelper (>= 10),
+   debhelper (>= 11),
javahelper,
gradle-debian-helper,
maven-repo-helper,
@@ -22,9 +22,9 @@ Build-Depends: default-jdk (>= 2:1.8),
default-jdk-doc,
libhtsjdk-java-doc,
libguava-java-doc
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/picard-tools.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/picard-tools.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/picard-tools
+Vcs-Git: https://salsa.debian.org/med-team/picard-tools.git
 Homepage: http://broadinstitute.github.io/picard/
 
 Package: picard-tools


=
debian/patches/10-build.xml.patch
=
--- a/debian/patches/10-build.xml.patch
+++ b/debian/patches/10-build.xml.patch
@@ -4,7 +4,7 @@ Forwarded: not-needed
 Last-Updated: 2016-07-07
 --- a/build.gradle
 +++ b/build.gradle
-@@ -12,13 +12,7 @@ plugins {
+@@ -12,13 +12,7 @@
  id "java"
  id 'maven'
  id 'signing'
@@ -18,7 +18,7 @@ Last-Updated: 2016-07-07
  }
  
  mainClassName = "picard.cmdline.PicardCommandLine"
-@@ -31,22 +25,6 @@ repositories {
+@@ -31,38 +25,31 @@
  }
  }
  
@@ -41,7 +41,14 @@ Last-Updated: 2016-07-07
  final htsjdkVersion = System.getProperty('htsjdk.version', '2.8.0')
  
  dependencies {
-@@ -60,9 +38,18 @@ dependencies {
+ compile 'com.google.guava:guava:15.0'
+ compile 'com.github.samtools:htsjdk:' + htsjdkVersion
+ //tools dependency for doclet requires sdk devel
+-compile(files(((URLClassLoader) 
ToolProvider.getSystemToolClassLoader()).getURLs()))
++//compile(files(((URLClassLoader) 
ToolProvider.getSystemToolClassLoader()).getURLs()))
+ testCompile 'org.testng:testng:6.9.10'
+ }
+ 
  sourceCompatibility = 1.8
  targetCompatibility = 1.8
  
@@ -62,7 +69,16 @@ Last-Updated: 2016-07-07
  
  logger.info("build for version:" + version)
  group = 'com.github.broadinstitute'
-@@ -323,19 +310,3 @@ task copyJavadoc(dependsOn: 'javadoc', t
+@@ -176,7 +163,7 @@
+ 
+ //generate documentation
+ 
+-task documentAll(dependsOn: ['documentCommands', 'createMetricsDoc', 
'documentStandardOptions']){
++task documentAll(dependsOn: ['documentCommands', 'documentStandardOptions']){
+   doFirst{
+ htmlDirInc.mkdirs()
+   }
+@@ -323,19 +310,3 @@
  from 'build/docs/javadoc'
  into "$htmlDir/javadoc"
  }


=
debian/patches/40-tests-fix-testng.patch
=
--- a/debian/patches/40-tests-fix-testng.patch
+++ b/debian/patches/40-tests-fix-testng.patch
@@ -3,7 +3,7 @@
 @@ -32,7 +32,7 @@
  compile 'com.github.samtools:htsjdk:' + htsjdkVersion
  //tools dependency for doclet requires sdk devel
- compile(files(((URLClassLoader) 
ToolProvider.getSystemToolClassLoader()).getURLs()))
+ //compile(files(((URLClassLoader) 
ToolProvider.getSystemToolClassLoader()).getURLs()))
 -testCompile 'org.testng:testng:6.9.10'
 +testCompile 'org.testng:testng:debian'
  }



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[med-svn] [Git][med-team/libbpp-core] Pushed new branch symbols_i386

2018-04-06 Thread Andreas Tille 
Andreas Tille pushed new branch symbols_i386 at Debian Med / libbpp-core

---
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[med-svn] [Git][med-team/tm-align][master] Updated RRID in d/u/metadata

2018-04-06 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / tm-align


Commits:
0e44d3fe by Steffen Möller at 2018-04-06T13:54:42+00:00
Updated RRID in d/u/metadata
- - - - -


1 changed file:

- debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -15,3 +15,10 @@ Reference:
  ISSN: 1362-4962
  DOI: 10.1093/nar/gki524
  PMID: 15849316
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_03646
+ - Name: bio.tools
+   Entry: NA
+ - Name: SciCrunch
+   Entry: NA



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https://salsa.debian.org/med-team/tm-align/commit/0e44d3fe005f6aeb815539040dc8bd8012307b1d

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[med-svn] [Git][med-team/perlprimer][master] Updated metadata

2018-04-06 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / perlprimer


Commits:
719011b2 by Steffen Möller at 2018-04-06T16:47:30+00:00
Updated metadata
- - - - -


1 changed file:

- debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -3,25 +3,26 @@ Contact: http://perlprimer.sourceforge.net/contact.html
 Homepage: http://perlprimer.sourceforge.net
 Name: PerlPrimer
 Reference:
- - author: Owen J. Marshall
-   title: >
+ - Author: Owen J. Marshall
+   Title: >
 PerlPrimer: cross-platform, graphical primer design for standard,
 bisulphite and real-time PCR
-   journal: Bioinformatics
-   volume: 20
-   number: 15
-   pages: 2471-2472
-   doi: 10.1093/bioinformatics/bth254
+   Journal: Bioinformatics
+   Volume: 20
+   Number: 15
+   Pages: 2471-2472
+   DOI: 10.1093/bioinformatics/bth254
PMID: 15073005
-   year: 2004
-   URL: 
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/15/2471
-   eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/20/15/2471.pdf
- - author: Owen J. Marshall
-   title: Graphical design of primers with PerlPrimer.
-   journal: Methods Mol Biol.
-   year: 2007
-   volume: 402
-   pages: 403-414
+   Year: 2004
+   URL: >
+http://bioinformatics.oxfordjournals.org/cgi/content/abstract/20/15/2471
+   ePrint: http://bioinformatics.oxfordjournals.org/cgi/reprint/20/15/2471.pdf
+ - Author: Owen J. Marshall
+   Title: Graphical design of primers with PerlPrimer.
+   Journal: Methods Mol Biol.
+   Year: 2007
+   Volume: 402
+   Pages: 403-414
PMID: 17951808
DOI: 10.1007/978-1-59745-528-2_21
URL: https://link.springer.com/protocol/10.1007%2F978-1-59745-528-2_21
@@ -30,6 +31,6 @@ Registry:
Entry: OMICS_02354
  - Name: bio.tools
Entry: NA
- - Name: RRID
+ - Name: SciCrunch
Entry: SCR_012038
 Screenshots: http://perlprimer.sourceforge.net/screenshots.html



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[med-svn] [Git][med-team/scoary][master] Updated RRID in d/u/metadata

2018-04-06 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / scoary


Commits:
d00eb7f7 by Steffen Möller at 2018-04-06T16:53:40+00:00
Updated RRID in d/u/metadata
- - - - -


1 changed file:

- debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -1,9 +1,17 @@
 Reference:
-  Author: Ola Brynildsrud and Jon Bohlin and Lonneke Scheffer and Vegard 
Eldholm
-  Title: Rapid scoring of genes in microbial pan-genome-wide association 
studies with Scoary
-  Journal: Genome Biology
-  Year: 2016
-  Volume: 17
-  Number: 238
-  DOI: 10.1186/s13059-016-1108-8
-  URL: 
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1108-8
+ Author: Ola Brynildsrud and Jon Bohlin and Lonneke Scheffer and Vegard Eldholm
+ Title: Rapid scoring of genes in microbial pan-genome-wide association 
studies with Scoary
+ Journal: Genome Biology
+ Year: 2016
+ Volume: 17
+ Number: 238
+ DOI: 10.1186/s13059-016-1108-8
+ URL: >
+  https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1108-8
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_13120
+ - Name: bio.tools
+   Entry: Scoary
+ - Name: SciCrunch
+   Entry: NA
\ No newline at end of file



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[med-svn] [Git][med-team/picard-tools] Pushed new tag debian/2.8.1+dfsg-4

2018-04-06 Thread Emmanuel Bourg 
Emmanuel Bourg pushed new tag debian/2.8.1+dfsg-4 at Debian Med / picard-tools

---
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[med-svn] [Git][med-team/spread-phy][master] Updated RRID in d/u/metadata

2018-04-06 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / spread-phy


Commits:
e4115fbb by Steffen Möller at 2018-04-06T16:28:29+00:00
Updated RRID in d/u/metadata
- - - - -


1 changed file:

- debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -2,15 +2,24 @@ Contact: Filip Bielejec 
 Homepage: http://www.kuleuven.be/aidslab/phylogeography/SPREAD.html
 Name: SPREAD
 Reference:
-  author: Filip Bielejec and Andrew Rambaut and Marc A. Suchard and Philippe 
Lemey
-  title: >
-SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics
-  journal: Bioinformatics
-  volume: 27
-  number: 20
-  pages: 2910-2912
-  year: 2011
-  PMID: 21911333
-  DOI: 10.1093/bioinformatics/btr481
-  URL: http://bioinformatics.oxfordjournals.org/content/27/20/2910.full
-  eprint: 
http://bioinformatics.oxfordjournals.org/content/early/2011/09/11/bioinformatics.btr481.full.pdf+html
+ Author: >
+  Filip Bielejec and Andrew Rambaut and Marc A. Suchard and Philippe Lemey
+ Title: >
+  SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics
+ Journal: Bioinformatics
+ Volume: 27
+ Number: 20
+ Pages: 2910-2912
+ Year: 2011
+ PMID: 21911333
+ DOI: 10.1093/bioinformatics/btr481
+ URL: http://bioinformatics.oxfordjournals.org/content/27/20/2910.full
+ ePrint: "http://bioinformatics.oxfordjournals.org/content/early/\
+  2011/09/11/bioinformatics.btr481.full.pdf+html"
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_08645
+ - Name: bio.tools
+   Entry: NA
+ - Name: SciCrunch
+   Entry: NA



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[med-svn] [Git][med-team/paleomix][master] Updated RRID in d/u/metadata

2018-04-06 Thread Steffen Möller 
Steffen Möller pushed to branch master at Debian Med / paleomix


Commits:
d308f958 by Steffen Möller at 2018-04-06T16:44:54+00:00
Updated RRID in d/u/metadata
- - - - -


1 changed file:

- debian/upstream/metadata


Changes:

=
debian/upstream/metadata
=
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -1,11 +1,23 @@
 Reference:
-  Author: Mikkel Schubert and Luca Ermini and Clio Der Sarkissian and Hákon 
Jónsson and Aurélien Ginolhac and Robert Schaefer and Michael D Martin and Ruth 
Fernández and Martin Kircher and Molly McCue and Eske Willerslev and Ludovic 
Orlando
-  Title: "Characterization of ancient and modern genomes by SNP detection and 
phylogenomic and metagenomic analysis using PALEOMIX"
-  Journal: Nature Protocols
-  Year: 2014
-  Volume: 9
-  Number: 5
-  Pages: 1056-82
-  DOI: 10.1038/nprot.2014.063
-  PMID: 24722405
-  URL: http://www.nature.com/nprot/journal/v9/n5/full/nprot.2014.063.html
+ Author: >
+  Mikkel Schubert and Luca Ermini and Clio Der Sarkissian and Hákon Jónsson and
+  Aurélien Ginolhac and Robert Schaefer and Michael D Martin and Ruth Fernández
+  and Martin Kircher and Molly McCue and Eske Willerslev and Ludovic Orlando
+ Title: >
+  Characterization of ancient and modern genomes by SNP detection and
+  phylogenomic and metagenomic analysis using PALEOMIX
+ Journal: Nature Protocols
+ Year: 2014
+ Volume: 9
+ Number: 5
+ Pages: 1056-82
+ DOI: 10.1038/nprot.2014.063
+ PMID: 24722405
+ URL: http://www.nature.com/nprot/journal/v9/n5/full/nprot.2014.063.html
+Registry:
+ - Name: OMICtools
+   Entry: OMICS_03749
+ - Name: SciCrunch
+   Entry: SCR_015057
+ - Name: bio.tools
+   Entry: PALEOMIX



View it on GitLab: 
https://salsa.debian.org/med-team/paleomix/commit/d308f95884314f4218040f89700f490c8551b7a5

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