[med-svn] [Git][med-team/bcbio][master] Update TODO - cthreadpool accepted, viennarna progressed

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / bcbio


Commits:
1e5c05c4 by Steffen Möller at 2019-09-11T21:50:04Z
Update TODO - cthreadpool accepted, viennarna progressed
- - - - -


1 changed file:

- debian/TODO


Changes:

=====================================
debian/TODO
=====================================
@@ -43,10 +43,6 @@ package libjs-scribl (in new queue) (in crash space)
     A surprisingly neat JavaScript library to show genomic features
        Needed for DFSG-compliance of seqcluster
 
-package cthreadpool (in new queue) (in crash space)
-   https://github.com/Pithikos/C-Thread-Pool/blob/master/thpool.h
-      Needed by ViennaRNA
-
 Package MutliQC (in crash space) (in new queue)
    https://salsa.debian.org/med-team/multiqc
      Addressed https://github.com/ewels/MultiQC/issues/800 by substuting
@@ -54,11 +50,25 @@ Package MutliQC (in crash space) (in new queue)
      The package was placed into contrib because of the dependency of its
      reports on external sources. For that reason and the remote depenency
      on ViennaRNA via seqcluster, also bcbio will be in contrib.
+     
+package pyutilib (in new queue) (in crash space)
+  https://github.com/PyUtilib/pyutilib
+  https://salsa.debian.org/python-team/modules/pyutilib
+    needed by pyomo for testing
 
 
 Packages just waiting for someone addressing the last mile for the upload
 -------------------------------------------------------------------------
 
+package viennarna (in crash space)
+    https://github.com/ViennaRNA/ViennaRNA
+    https://salsa.debian.org/med-team/vienna-rna/blob/master/debian/changelog
+       The package now has a custom license file - redistributable but non-free.
+    Needed for testing seqcluster.
+    Python and Perl packages are not tested, yet, not needed for seqcluster
+    Package likely to be uploadable to non-free. Final checks needed.
+    Documentation no longer builds with 2.4.14 would be nice to reactivate but not ultimately important for first upload.
+
 package pyomo (in crash space)
   https://github.com/Pyomo/pyomo
   https://salsa.debian.org/science-team/pyomo
@@ -66,11 +76,6 @@ package pyomo (in crash space)
     needed by optitype
     Status: Builds if errors in build time tests will be ignored
 
-package pyutilib (in new queue) (in crash space)
-  https://github.com/PyUtilib/pyutilib
-  https://salsa.debian.org/python-team/modules/pyutilib
-    needed by pyomo for testing
-
 package python-seqcluster (in crash space)
    https://github.com/lpantano/seqcluster/
    https://salsa.debian.org/med-team/python-seqcluster
@@ -100,17 +105,6 @@ package python-seqcluster (in crash space)
        apparently optional for bcbio: r-bioc-isomiRs - (needs r-bioc-DEGreport) all pre-depends except edgeR are in new
        apparently optional for bcbio: install_github('rstudio/rmarkdown')  -- this may be the same we have from CRAN - not checked
 
-package viennarna (in crash space)
-    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.
-	Steffen revisits ViennaRNA, will update to new upstream version this weekend
-           Using current master not release because of erroneous commits of autogenerated files in 2.4.13 release source tree.
-           Manual removal of folders along instructions in d/copyright
-    Python and Perl packages are not functional, yet, not needed for seqcluster
-    Waiting for acceptance of cthreadpool.
 
 Packages presumed easy to package
 ---------------------------------



View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/1e5c05c402d8e7a25c7a71834491c3d016b24154

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View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/1e5c05c402d8e7a25c7a71834491c3d016b24154
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