[med-svn] [Git][med-team/trinityrnaseq][master] 15 commits: New upstream version 2.8.6+dfsg

[Michael R. Crusoe]

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


Commits:
2831268b by Michael R. Crusoe at 2019-10-14T10:49:01+02:00
New upstream version 2.8.6+dfsg
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1412d7f7 by Michael R. Crusoe at 2020-04-26T16:55:52+02:00
add build-dep on r-bioc-rots

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8cbef3e0 by Michael R. Crusoe at 2020-04-26T17:01:55+02:00
routine-update: New upstream version

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1c446ac5 by Michael R. Crusoe at 2020-04-26T17:02:08+02:00
New upstream version 2.10.0+dfsg
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823be8fb by Michael R. Crusoe at 2020-04-26T17:05:43+02:00
Update upstream source from tag 'upstream/2.10.0+dfsg'

Update to upstream version '2.10.0+dfsg'
with Debian dir b5013a0629527e43eef7003a3144fb2349436359
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f11e454c by Michael R. Crusoe at 2020-04-26T17:05:43+02:00
routine-update: Standards-Version: 4.5.0

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bf83f7dd by Michael R. Crusoe at 2020-04-26T17:31:06+02:00
Refresh patches

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cdd32fba by Michael R. Crusoe at 2020-04-26T17:31:40+02:00
routine-update: Add salsa-ci file

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64eb0ca4 by Michael R. Crusoe at 2020-04-26T17:31:41+02:00
routine-update: Rules-Requires-Root: no

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097cb276 by Michael R. Crusoe at 2020-04-26T17:41:31+02:00
Use secure URI in Homepage field.

Fixes: lintian: homepage-field-uses-insecure-uri
See-also: https://lintian.debian.org/tags/homepage-field-uses-insecure-uri.html

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7b171d3b by Michael R. Crusoe at 2020-04-26T18:20:50+02:00
debian/rules: seqtk-trinity now has a unversioned path

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44e5a36e by Michael R. Crusoe at 2020-04-26T18:24:26+02:00
debian/patches/butterfly: restore missing Butterfly sources

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e9f74728 by Michael R. Crusoe at 2020-04-26T19:05:40+02:00
many more deps

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a50c58bf by Michael R. Crusoe at 2020-04-26T23:23:19+02:00
Install the new bamsfilter plugin

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550d8458 by Michael R. Crusoe at 2020-04-26T23:33:43+02:00
fixup heatmap

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30 changed files:

- .gitmodules
- Analysis/DifferentialExpression/Glimma.Trinity.Rscript
- Analysis/DifferentialExpression/PtR
- + Analysis/DifferentialExpression/R/edgeR.TMM.minimal.R
- Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl
- Analysis/DifferentialExpression/run_DE_analysis.pl
- Analysis/DifferentialExpression/run_GOseq.pl
- Analysis/DifferentialExpression/run_TMM_normalization_write_FPKM_matrix.pl
- Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py
- Analysis/SuperTranscripts/DTU/dexseq_wrapper.pl
- Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py
- Analysis/SuperTranscripts/pylib/Node_alignment.py
- − Butterfly/.err
- + Butterfly/README.md
- − Butterfly/build_jar.xml
- − Butterfly/src/.classpath
- − Butterfly/src/.err
- − Butterfly/src/.project
- − Butterfly/src/.settings/org.eclipse.jdt.core.prefs
- − Butterfly/src/README
- − Butterfly/src/_t_seqA.fa
- − Butterfly/src/_t_seqB.fa
- − Butterfly/src/build.xml
- − Butterfly/src/runExample.sh
- − Butterfly/src/run_NWalign.sh
- − Butterfly/src/run_butterfly_nonJar.sh
- − Butterfly/src/sample_data/c1.graph.out
- − Butterfly/src/sample_data/c1.graph.reads
- − Butterfly/src/src/AlignmentStats.java
- − Butterfly/src/src/BFLY_GLOBALS.java


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/d1a9ff02b65a7ffb7f064617b45dd1f53c1a203a...550d8458ef63ffaeb289c1e494e99962051a1ea9

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View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/d1a9ff02b65a7ffb7f064617b45dd1f53c1a203a...550d8458ef63ffaeb289c1e494e99962051a1ea9
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