[med-svn] [Git][med-team/community/helper-scripts][master] automatic update

Andreas Tille (@tille) gitlab at salsa.debian.org
Thu Jun 17 14:42:24 BST 2021



Andreas Tille pushed to branch master at Debian Med / community / helper-scripts


Commits:
19aa5d0f by Andreas Tille at 2021-06-17T13:42:20+00:00
automatic update

- - - - -


2 changed files:

- debian-med-tests.txt
- outdated_med-packages.txt


Changes:

=====================================
debian-med-tests.txt
=====================================
@@ -1,73 +1,79 @@
-Last-Update: Thu, 17 Jun 2021 01:42:03 +0000
+Last-Update: Thu, 17 Jun 2021 13:42:03 +0000
 
  Source                        | Vote   |     Tasks                                           |                                 Tags                                 
 -------------------------------+--------+-----------------------------------------------------+----------------------------------------------------------------------
- dcmtk                         |    172 | {imaging,covid-19}                                  | 
- orthanc                       |     90 | {practice,imaging,covid-19}                         | 
- orthanc-wsi                   |     47 | {oncology,his,imaging,covid-19,practice,laboratory} | 
- gdcm                          |     41 | {imaging-dev}                                       | 
+ dcmtk                         |    173 | {covid-19,imaging}                                  | 
+ orthanc                       |     90 | {imaging,covid-19,practice}                         | 
+ orthanc-wsi                   |     47 | {oncology,laboratory,imaging,covid-19,his,practice} | 
+ gdcm                          |     42 | {imaging-dev}                                       | 
  htsjdk                        |     32 | {bio-dev}                                           | 
  amide                         |     27 | {imaging}                                           | 
- dicom3tools                   |     27 | {imaging}                                           | 
+ dicom3tools                   |     26 | {imaging}                                           | 
  openslide                     |     25 | {imaging}                                           | 
- dicomscope                    |     21 | {imaging}                                           | 
  dcm2niix                      |     19 | {imaging}                                           | 
- adun.app                      |     16 | {bio}                                               | 
- ngs-sdk                       |     15 | {bio-dev}                                           | 
- odin                          |     15 | {imaging-dev,imaging}                               | 
- gdcm                          |     14 | {imaging,covid-19}                                  | 
- invesalius                    |     14 | {imaging}                                           | 
+ dicomscope                    |     19 | {imaging}                                           | 
+ adun.app                      |     17 | {bio}                                               | 
+ ngs-sdk                       |     16 | {bio-dev}                                           | 
+ odin                          |     16 | {imaging,imaging-dev}                               | 
+ invesalius                    |     15 | {imaging}                                           | 
+ gdcm                          |     14 | {covid-19,imaging}                                  | 
  minc-tools                    |     14 | {imaging}                                           | 
- gnumed-server                 |     13 | {covid-19,practice}                                 | 
+ gnumed-server                 |     13 | {practice,covid-19}                                 | 
  insighttoolkit4               |     13 | {imaging-dev}                                       | 
  dicomnifti                    |     12 | {imaging}                                           | 
  orthanc-webviewer             |     12 | {imaging}                                           | 
  gdcm                          |     11 | {imaging-dev}                                       | 
  nifticlib                     |     11 | {imaging}                                           | 
  pixelmed                      |     10 | {imaging}                                           | 
- ngs-sdk                       |      9 | {bio-dev}                                           | 
  plastimatch                   |      9 | {imaging}                                           | 
  ea-utils                      |      8 | {bio}                                               | 
  melting                       |      8 | {cloud,bio}                                         | 
+ ngs-sdk                       |      8 | {bio-dev}                                           | 
  salmon                        |      8 | {covid-19,bio}                                      | 
+ biojava-live                  |      7 | {bio-dev}                                           | 
+ jebl2                         |      7 | {bio-dev}                                           | 
  librg-utils-perl              |      7 | {bio}                                               | 
  mia                           |      7 | {imaging}                                           | 
  runcircos-gui                 |      7 | {bio}                                               | 
- biojava-live                  |      6 | {bio-dev}                                           | 
- jebl2                         |      6 | {bio-dev}                                           | 
- king                          |      6 | {imaging,typesetting}                               | 
+ staden                        |      7 | {bio}                                               | 
+ bio-tradis                    |      6 | {bio,bio-dev}                                       | 
+ king                          |      6 | {typesetting,imaging}                               | 
  ngs-sdk                       |      6 | {bio-dev}                                           | 
  nifti2dicom                   |      6 | {imaging}                                           | 
  openslide                     |      6 | {imaging-dev}                                       | 
- stacks                        |      6 | {bio}                                               | 
- staden                        |      6 | {bio}                                               | 
- treeview                      |      6 | {bio-phylogeny,bio}                                 | 
- bio-tradis                    |      5 | {bio-dev,bio}                                       | 
- busco                         |      5 | {covid-19,bio}                                      | 
+ treeview                      |      6 | {bio,bio-phylogeny}                                 | 
+ bitseq                        |      5 | {bio}                                               | 
+ blasr                         |      5 | {bio,bio-ngs}                                       | 
+ brig                          |      5 | {bio}                                               | 
+ busco                         |      5 | {bio,covid-19}                                      | 
+ embassy-domainatrix           |      5 | {cloud,bio}                                         | 
+ embassy-domalign              |      5 | {cloud,bio}                                         | 
  lagan                         |      5 | {bio}                                               | 
  obitools                      |      5 | {bio}                                               | 
- orthanc-dicomweb              |      5 | {imaging,covid-19}                                  | 
+ orthanc-dicomweb              |      5 | {covid-19,imaging}                                  | 
  saint                         |      5 | {bio}                                               | 
  salmid                        |      5 | {bio}                                               | 
  spread-phy                    |      5 | {bio,bio-phylogeny}                                 | 
- anfo                          |      4 | {cloud,bio}                                         | 
- arden                         |      4 | {cloud,bio}                                         | 
+ stacks                        |      5 | {bio}                                               | 
+ anfo                          |      4 | {bio,cloud}                                         | 
+ arden                         |      4 | {bio,cloud}                                         | 
  assemblytics                  |      4 | {bio}                                               | 
- bamkit                        |      4 | {bio,covid-19}                                      | 
+ bamkit                        |      4 | {covid-19,bio}                                      | 
  beast-mcmc                    |      4 | {bio-phylogeny,bio}                                 | 
- bitseq                        |      4 | {bio}                                               | 
- blasr                         |      4 | {bio,bio-ngs}                                       | 
- brig                          |      4 | {bio}                                               | 
+ canu                          |      4 | {bio}                                               | 
  dicompyler                    |      4 | {oncology}                                          | 
  elastix                       |      4 | {imaging}                                           | 
- embassy-domainatrix           |      4 | {cloud,bio}                                         | 
- embassy-domalign              |      4 | {cloud,bio}                                         | 
+ embassy-domsearch             |      4 | {cloud,bio}                                         | 
+ emboss-explorer               |      4 | {bio}                                               | 
+ gatb-core                     |      4 | {bio}                                               | 
  getdata                       |      4 | {bio}                                               | 
  jellyfish1                    |      4 | {bio}                                               | 
  lamarc                        |      4 | {bio}                                               | 
  libdivsufsort                 |      4 | {bio-dev}                                           | 
  libminc                       |      4 | {imaging-dev}                                       | 
  libncl                        |      4 | {bio}                                               | 
+ librdp-taxonomy-tree-java     |      4 | {bio-dev}                                           | 
+ mhap                          |      4 | {bio,bio-ngs}                                       | 
  orthanc-postgresql            |      4 | {imaging}                                           | 
  phast                         |      4 | {bio}                                               | 
  phyutility                    |      4 | {cloud,bio}                                         | 
@@ -76,8 +82,9 @@ Last-Update: Thu, 17 Jun 2021 01:42:03 +0000
  prime-phylo                   |      4 | {cloud,bio}                                         | 
  quorum                        |      4 | {bio}                                               | 
  rdp-alignment                 |      4 | {bio}                                               | 
+ rdp-classifier                |      4 | {bio}                                               | 
  sambamba                      |      4 | {bio}                                               | 
- sibsim4                       |      4 | {cloud,bio}                                         | 
+ sibsim4                       |      4 | {bio,cloud}                                         | 
  sight                         |      4 | {imaging}                                           | 
  spaced                        |      4 | {bio}                                               | 
  tracetuner                    |      4 | {bio}                                               | 
@@ -85,38 +92,31 @@ Last-Update: Thu, 17 Jun 2021 01:42:03 +0000
  zalign                        |      4 | {cloud,bio}                                         | 
  bart-view                     |      3 | {imaging}                                           | 
  biomaj3-cli                   |      3 | {cloud}                                             | 
- canu                          |      3 | {bio}                                               | 
  clonalframeml                 |      3 | {covid-19,bio}                                      | 
  clonalorigin                  |      3 | {bio}                                               | 
  ecopcr                        |      3 | {bio}                                               | 
- embassy-domsearch             |      3 | {cloud,bio}                                         | 
- emboss-explorer               |      3 | {bio}                                               | 
  estscan                       |      3 | {bio}                                               | 
  fastml                        |      3 | {bio}                                               | 
  fsm-lite                      |      3 | {bio}                                               | 
- gatb-core                     |      3 | {bio}                                               | 
  ghmm                          |      3 | {bio}                                               | 
  ipig                          |      3 | {bio}                                               | 
- jmodeltest                    |      3 | {bio,bio-phylogeny}                                 | 
+ jmodeltest                    |      3 | {bio-phylogeny,bio}                                 | 
  libpal-java                   |      3 | {bio-dev}                                           | 
- librdp-taxonomy-tree-java     |      3 | {bio-dev}                                           | 
  libsbml                       |      3 | {bio-dev}                                           | 
  logol                         |      3 | {bio}                                               | 
  mauve-aligner                 |      3 | {bio}                                               | 
- mhap                          |      3 | {bio-ngs,bio}                                       | 
  microbegps                    |      3 | {bio}                                               | 
  nifticlib                     |      3 | {imaging-dev}                                       | 
- nipype                        |      3 | {imaging,imaging-dev}                               | 
+ nipype                        |      3 | {imaging-dev,imaging}                               | 
  orthanc-mysql                 |      3 | {imaging}                                           | 
- oscar                         |      3 | {tools,practice,data}                               | 
- paraclu                       |      3 | {cloud,bio}                                         | 
+ oscar                         |      3 | {tools,data,practice}                               | 
+ paraclu                       |      3 | {bio,cloud}                                         | 
  pbdagcon                      |      3 | {bio}                                               | 
  perm                          |      3 | {bio,cloud}                                         | 
- proalign                      |      3 | {bio-phylogeny,bio}                                 | 
+ proalign                      |      3 | {bio,bio-phylogeny}                                 | 
  pymia                         |      3 | {imaging-dev}                                       | 
  rambo-k                       |      3 | {bio}                                               | 
- rdp-classifier                |      3 | {bio}                                               | 
- rtax                          |      3 | {cloud,bio}                                         | 
+ rtax                          |      3 | {bio,cloud}                                         | 
  sga                           |      3 | {bio}                                               | 
  soapaligner                   |      3 | {bio}                                               | 
  soapsnp                       |      3 | {bio}                                               | 
@@ -125,7 +125,7 @@ Last-Update: Thu, 17 Jun 2021 01:42:03 +0000
  surankco                      |      3 | {bio}                                               | 
  tvc                           |      3 | {bio}                                               | 
  blimps                        |      2 | {bio}                                               | 
- delly                         |      2 | {covid-19,bio}                                      | 
+ delly                         |      2 | {bio,covid-19}                                      | 
  hinge                         |      2 | {bio}                                               | 
  metaphlan2                    |      2 | {bio}                                               | 
  orthanc-gdcm                  |      2 | {imaging}                                           | 
@@ -139,7 +139,7 @@ Last-Update: Thu, 17 Jun 2021 01:42:03 +0000
  atropos                       |      1 | {bio}                                               | 
  cat-bat                       |      1 | {bio,covid-19}                                      | 
  htscodecs                     |      1 | {covid-19,bio-dev}                                  | 
- intake                        |      1 | {bio-dev,bio}                                       | 
+ intake                        |      1 | {bio,bio-dev}                                       | 
  kmerresistance                |      1 | {bio}                                               | 
  libbio-mage-utils-perl        |      1 | {bio-dev}                                           | 
  libchado-perl                 |      1 | {bio-dev}                                           | 
@@ -150,7 +150,7 @@ Last-Update: Thu, 17 Jun 2021 01:42:03 +0000
  opencfu                       |      1 | {laboratory}                                        | 
  orthanc-python                |      1 | {covid-19}                                          | 
  parallel-fastq-dump           |      1 | {covid-19}                                          | 
- plasmidid                     |      1 | {covid-19,bio}                                      | 
+ plasmidid                     |      1 | {bio,covid-19}                                      | 
  python-wdlparse               |      1 | {bio-dev}                                           | 
  samtools-legacy               |      1 | {bio-dev}                                           | 
  simpleitk                     |      1 | {imaging-dev}                                       | 
@@ -190,8 +190,9 @@ Last-Update: Thu, 17 Jun 2021 01:42:03 +0000
  libgenome                     |      0 | {bio-dev}                                           | 
  libgkarrays                   |      0 | {bio-dev}                                           | 
  libhmsbeagle                  |      0 | {bio-dev}                                           | 
- libics                        |      0 | {covid-19,imaging-dev}                              | 
+ libics                        |      0 | {imaging-dev,covid-19}                              | 
  libjloda-java                 |      0 | {bio-dev}                                           | 
+ libmaus2                      |      0 | {bio-dev,covid-19}                                  | 
  libmems                       |      0 | {bio-dev}                                           | 
  libmialm                      |      0 | {imaging-dev}                                       | 
  libncl                        |      0 | {bio-dev}                                           | 
@@ -211,14 +212,14 @@ Last-Update: Thu, 17 Jun 2021 01:42:03 +0000
  orthanc-imagej                |      0 | {imaging}                                           | 
  pbcopper                      |      0 | {bio-dev}                                           | 
  pbseqlib                      |      0 | {bio-dev}                                           | 
- pigx-rnaseq                   |      0 | {bio,covid-19}                                      | 
+ pigx-rnaseq                   |      0 | {covid-19,bio}                                      | 
  pilercr                       |      0 | {bio}                                               | 
  pique                         |      0 | {bio}                                               | 
- pplacer                       |      0 | {bio,covid-19,bio-phylogeny}                        | 
+ pplacer                       |      0 | {covid-19,bio,bio-phylogeny}                        | 
  python-bcbio-gff              |      0 | {bio-dev}                                           | 
  python-epimodels              |      0 | {epi}                                               | 
- python-seqcluster             |      0 | {covid-19,bio-dev}                                  | 
- q2-sample-classifier          |      0 | {bio,bio-dev}                                       | 
+ python-seqcluster             |      0 | {bio-dev,covid-19}                                  | 
+ q2-sample-classifier          |      0 | {bio-dev,bio}                                       | 
  resfinder-db                  |      0 | {bio}                                               | 
  sbmltoolbox                   |      0 | {bio-dev}                                           | 
  seq-gen                       |      0 | {bio}                                               | 
@@ -232,8 +233,7 @@ Last-Update: Thu, 17 Jun 2021 01:42:03 +0000
  trace2dbest                   |      0 | {bio}                                               | 
  varna                         |      0 | {bio}                                               | 
  xdffileio                     |      0 | {imaging-dev}                                       | 
- yanagiba                      |      0 | {covid-19,bio}                                      | 
- libmaus2                      |     -1 | {bio-dev,covid-19}                                  | 
+ yanagiba                      |      0 | {bio,covid-19}                                      | 
  mssstest                      |     -1 | {tools}                                             | 
  python-seqcluster             |     -1 | {bio}                                               | 
  sight                         |     -1 | {imaging-dev}                                       | 


=====================================
outdated_med-packages.txt
=====================================
The diff for this file was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/19aa5d0f0b57d8dbf18491e5570156f6b2704f0e

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View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/19aa5d0f0b57d8dbf18491e5570156f6b2704f0e
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