[med-svn] [Git][med-team/bcbio][master] Update of d/TODO, d/control

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / bcbio


Commits:
86cdb51c by Steffen Möller at 2019-06-03T16:25:32Z
Update of d/TODO, d/control

- - - - -


2 changed files:

- debian/TODO
- debian/control


Changes:

=====================================
debian/TODO
=====================================
@@ -29,7 +29,21 @@ package optitype
 
 package pyomo
   https://github.com/Pyomo/pyomo
-  needed by optitype
+  https://salsa.debian.org/python-team/applications/pyomo - builds locally (Steffen does not have upload privileges, some tests fail)
+    needed by optitype
+
+package pyutilib
+  https://github.com/PyUtilib/pyutilib
+  https://salsa.debian.org/python-team/modules/pyutilib - builds, tests fail
+    needed by pyomo for testing
+
+package gjh_asl_json
+  https://github.com/ghackebeil/gjh_asl_json
+    needed by pyomo for testing
+
+package "asl solver"
+  http://www.ampl.com/netlib/ampl/solvers.tgz
+    needed by gjh_asl_json
 
 package vcfanno
   https://salsa.debian.org/med-team/vcfanno
@@ -65,14 +79,15 @@ package Python module geneimpacts
    https://salsa.debian.org/med-team/python-geneimpacts (in new queue)
 
 package seqcluster
-https://github.com/lpantano/seqcluster/archive/1824d37.tar.gz
+   https://github.com/lpantano/seqcluster/archive/1824d37.tar.gz
 
 package pizzly
-https://github.com/pmelsted/pizzly
-including pizzly_flatten_json.py
+   https://github.com/pmelsted/pizzly
+   including pizzly_flatten_json.py
+     Steffen has a look
 
 package vt
-https://github.com/atks/vt
+   https://github.com/atks/vt
 
 package fgbio
   https://github.com/fulcrumgenomics/fgbio


=====================================
debian/control
=====================================
@@ -90,6 +90,7 @@ Recommends: bcftools,
             grabix,
             libvcflib-tools,
             macs,
+            python3-geneimpacts,
             python3-h5py,
             pythonpy,
             rna-star,



View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/86cdb51ceb37ac51305573d5382165c295f33541

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View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/86cdb51ceb37ac51305573d5382165c295f33541
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