[med-svn] [Git][med-team/bcbio][master] seqcluster needs ViennaRNA

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / bcbio


Commits:
0cd543d3 by Steffen Möller at 2019-06-20T10:13:05Z
seqcluster needs ViennaRNA

- - - - -


1 changed file:

- debian/TODO


Changes:

=====================================
debian/TODO
=====================================
@@ -65,15 +65,29 @@ package pyutilib
 package seqcluster
    https://github.com/lpantano/seqcluster/archive/1824d37.tar.gz
    https://salsa.debian.org/med-team/python-seqcluster
-      Some nitty-gritty was going on there wrt Python3 transition
-      and an upcoming new release. Needs another review and
-      likely some communication with upstream.
-         Steffen addresses this.
-
+      The Python3 transition seems fine now. Weird, though,
+      the test takes too long / something hangs.
+      When grepping for "conda install":
+       ./doc/source/installation.rst:    ~/install/seqcluster/anaconda/conda install seqcluster seqbuster bedtools samtools pip nose numpy scipy pandas pyvcf -c bioconda
+       ./Dockerfile:     conda install --yes -c conda-forge -c bioconda scipy seqcluster bedtools samtools pip nose setuptools -q && \
+       ./.travis.yml:- conda install --yes -c conda-forge -c bioconda memory_profiler openjdk pysam pybedtools pandas numpy biopython progressbar2 pyyaml bedtools samtools mirtop viennarna -q
+      so, for some successful testing it seems like we need viennarna, still. That is not yet in the distribution. If truly dependending on it then bcbio ends up in contrib.
+
+package viennarna
+    https://github.com/ViennaRNA/ViennaRNA
+    https://salsa.debian.org/med-team/vienna-rna/blob/master/debian/changelog
+       No idea about where exactly we stand with this.
+       The package now has a custom license file - redistributable but non-free.
+    Needed for testing seqcluster.
 
 Packages presumed easy to package
 ---------------------------------
 
+package Scribl
+  http://chmille4.github.io/Scribl/
+    A surprisingly neat JavaScript library to show genomic features
+       Needed for seqcluster
+
 package gjh_asl_json
   https://github.com/ghackebeil/gjh_asl_json
     needed by pyomo for testing



View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/0cd543d3cc66fa1bc70dc90a9b82b894478c2eac

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