debian/changelog

-debian-med (3.5.1) UNRELEASED; urgency=medium
+debian-med (3.5.1) unstable; urgency=medium
 
   * Drop fastx-toolkit and libgtextutils since unmaintained and
     libgtextutils has issued with gcc9
+  * Drop mgltools-pmv which is constantly broken for several years
 
- -- Andreas Tille <tille@debian.org>  Mon, 02 Dec 2019 09:54:51 +0100
+  * start of automatic changelog entry * 
+  
+  * Changes in metapackage dependencies
+   -med-bio
+    added:
+      Recommends:  r-bioc-geoquery, r-cran-wgcna
+    removed:
+      Recommends:  mgltools-pmv, r-other-wgcna, fastx-toolkit
+   -med-bio-dev
+    added:
+      Suggests:  r-bioc-geoquery
+    removed:
+      Suggests:  libgtextutils-dev
+   -med-bio-ngs
+    removed:
+      Recommends:  fastx-toolkit
+   -med-cloud
+    removed:
+      Recommends:  fastx-toolkit
+
+ -- Andreas Tille <tille@debian.org>  Fri, 06 Dec 2019 18:24:39 +0100
 
 debian-med (3.5) unstable; urgency=medium
 

debian/control

@@ -211,7 +211,6 @@ Recommends: abacas,
             fastqc,
             fastqtl,
             fasttree,
-            fastx-toolkit,
             ffindex,
             figtree,
             fitgcp,
@@ -543,7 +542,6 @@ Recommends: abacas,
             theseus,
             tigr-glimmer,
             tm-align,
-            tnseq-transit,
             toil,
             topp,
             toppred,
@@ -690,7 +688,6 @@ Suggests: acacia,
           metastudent-data-2,
           metastudent-data-3,
           mgltools-cadd,
-          mgltools-pmv,
           mgltools-vision,
           migrate,
           mindthegap,
@@ -784,6 +781,7 @@ Suggests: acacia,
           r-bioc-annotationhub,
           r-bioc-aroma.light,
           r-bioc-ensembldb,
+          r-bioc-geoquery,
           r-bioc-go.db,
           r-bioc-metagenomeseq,
           r-bioc-mofa,
@@ -803,8 +801,8 @@ Suggests: acacia,
           r-cran-sctransform,
           r-cran-seurat,
           r-cran-tsne,
+          r-cran-wgcna,
           r-other-apmswapp,
-          r-other-wgcna,
           raccoon,
           ragout,
           raxml-ng,
@@ -851,6 +849,7 @@ Suggests: acacia,
           tide,
           tigr-glimmer-mg,
           tn-seqexplorer,
+          tnseq-transit,
           treebuilder3d,
           treetime,
           trim-galore,
@@ -896,6 +895,7 @@ Recommends: bio-tradis,
             libbio-coordinate-perl,
             libbio-das-lite-perl,
             libbio-eutilities-perl,
+            libbio-graphics-perl,
             libbio-mage-perl,
             libbio-mage-utils-perl,
             libbio-primerdesigner-perl,
@@ -1020,7 +1020,6 @@ Recommends: bio-tradis,
             python3-rdkit,
             python3-ruffus,
             python3-screed,
-            python3-skbio,
             python3-sqt,
             python3-treetime,
             r-bioc-biobase,
@@ -1060,7 +1059,6 @@ Suggests: biobambam2,
           galaxy-lib,
           libbam-dev,
           libbigwig-dev,
-          libbio-graphics-perl,
           libbiod-dev,
           libdisorder-dev,
           libfast-perl,
@@ -1068,7 +1066,6 @@ Suggests: biobambam2,
           libfreecontact-doc,
           libgclib,
           libgoby-java,
-          libgtextutils-dev,
           libmaus2-dev,
           libmilib-java,
           libmodhmm-dev,
@@ -1110,6 +1107,7 @@ Suggests: biobambam2,
           python3-pyflow,
           python3-roadrunner,
           python3-seqcluster,
+          python3-skbio,
           r-bioc-affy,
           r-bioc-affyio,
           r-bioc-altcdfenvs,
@@ -1137,6 +1135,7 @@ Suggests: biobambam2,
           r-bioc-genomicalignments,
           r-bioc-genomicfeatures,
           r-bioc-genomicranges,
+          r-bioc-geoquery,
           r-bioc-go.db,
           r-bioc-graph,
           r-bioc-gviz,
@@ -1244,7 +1243,6 @@ Recommends: abyss,
             fastlink,
             fastqc,
             fasttree,
-            fastx-toolkit,
             fitgcp,
             flexbar,
             freecontact,
@@ -1605,7 +1603,6 @@ Recommends: cimg-dev,
             libbart-dev,
             libcifti-dev,
             libedf-dev,
-            libgdcm2-dev,
             libgdf-dev,
             libgiftiio-dev,
             libinsighttoolkit4-dev,
@@ -1646,6 +1643,7 @@ Suggests: emokit,
           libcv-dev,
           libeegdev-dev,
           libfreeimage-dev,
+          libgdcm2-dev,
           libics-dev,
           liblimereg-dev,
           libmni-perllib-perl,

tasks/bio

@@ -211,7 +211,7 @@ Recommends: autogrid
 
 Recommends: autodock-vina
 
-Recommends: autodocktools, mgltools-pmv, mgltools-vision, mgltools-cadd
+Recommends: autodocktools, mgltools-vision, mgltools-cadd
 
 Recommends: mustang