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

Andreas Tille (@tille) gitlab at salsa.debian.org
Fri Jul 16 14:42:25 BST 2021



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


Commits:
e0e332ac by Andreas Tille at 2021-07-16T13:42:21+00:00
automatic update

- - - - -


2 changed files:

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


Changes:

=====================================
debian-med-tests.txt
=====================================
@@ -1,164 +1,135 @@
-Last-Update: Fri, 16 Jul 2021 01:42:04 +0000
+Last-Update: Fri, 16 Jul 2021 13:42:04 +0000
 
  Source                        | Vote   |     Tasks                                           |                                 Tags                                 
 -------------------------------+--------+-----------------------------------------------------+----------------------------------------------------------------------
- dcmtk                         |    167 | {covid-19,imaging}                                  | 
- orthanc                       |     88 | {imaging,covid-19,practice}                         | 
- orthanc-wsi                   |     48 | {imaging,practice,his,covid-19,oncology,laboratory} | 
- gdcm                          |     39 | {imaging-dev}                                       | 
- dicomscope                    |     29 | {imaging}                                           | 
+ dcmtk                         |    169 | {covid-19,imaging}                                  | 
+ orthanc                       |     89 | {imaging,covid-19,practice}                         | 
+ orthanc-wsi                   |     49 | {imaging,practice,his,covid-19,oncology,laboratory} | 
+ gdcm                          |     38 | {imaging-dev}                                       | 
+ dicomscope                    |     30 | {imaging}                                           | 
  dicom3tools                   |     27 | {imaging}                                           | 
  amide                         |     26 | {imaging}                                           | 
- dcm2niix                      |     25 | {imaging}                                           | 
- htsjdk                        |     25 | {bio-dev}                                           | 
+ dcm2niix                      |     24 | {imaging}                                           | 
  gdcm                          |     21 | {covid-19,imaging}                                  | 
+ htsjdk                        |     21 | {bio-dev}                                           | 
  odin                          |     17 | {imaging-dev,imaging}                               | 
- ngs-sdk                       |     14 | {bio-dev}                                           | 
  minc-tools                    |     13 | {imaging}                                           | 
  orthanc-webviewer             |     13 | {imaging}                                           | 
  gnumed-server                 |     12 | {covid-19,practice}                                 | 
  pixelmed                      |     12 | {imaging}                                           | 
  dicomnifti                    |     11 | {imaging}                                           | 
  insighttoolkit4               |     11 | {imaging-dev}                                       | 
+ ngs-sdk                       |     11 | {bio-dev}                                           | 
  gdcm                          |     10 | {imaging-dev}                                       | 
  invesalius                    |     10 | {imaging}                                           | 
  nifticlib                     |     10 | {imaging}                                           | 
- adun.app                      |      9 | {bio}                                               | 
  openslide                     |      9 | {imaging}                                           | 
+ adun.app                      |      8 | {bio}                                               | 
  plastimatch                   |      8 | {imaging}                                           | 
  libminc                       |      7 | {imaging-dev}                                       | 
  mia                           |      7 | {imaging}                                           | 
  ngs-sdk                       |      7 | {bio-dev}                                           | 
  dicompyler                    |      6 | {oncology}                                          | 
- ea-utils                      |      6 | {bio}                                               | 
  libdivsufsort                 |      6 | {bio-dev}                                           | 
  nifti2dicom                   |      6 | {imaging}                                           | 
  nifticlib                     |      6 | {imaging-dev}                                       | 
- busco                         |      5 | {bio,covid-19}                                      | 
- jebl2                         |      5 | {bio-dev}                                           | 
- king                          |      5 | {imaging,typesetting}                               | 
- librg-utils-perl              |      5 | {bio}                                               | 
+ oscar                         |      6 | {tools,data,practice}                               | 
+ ea-utils                      |      5 | {bio}                                               | 
  nifti2dicom                   |      5 | {imaging}                                           | 
  openslide                     |      5 | {imaging-dev}                                       | 
  orthanc-postgresql            |      5 | {imaging}                                           | 
- oscar                         |      5 | {tools,data,practice}                               | 
- salmid                        |      5 | {bio}                                               | 
  sight                         |      5 | {imaging}                                           | 
- treeview                      |      5 | {bio-phylogeny,bio}                                 | 
- ngs-sdk                       |      4 | {bio-dev}                                           | 
+ busco                         |      4 | {bio,covid-19}                                      | 
+ jebl2                         |      4 | {bio-dev}                                           | 
+ king                          |      4 | {imaging,typesetting}                               | 
+ librg-utils-perl              |      4 | {bio}                                               | 
  orthanc-dicomweb              |      4 | {covid-19,imaging}                                  | 
- runcircos-gui                 |      4 | {bio}                                               | 
- stacks                        |      4 | {bio}                                               | 
+ salmid                        |      4 | {bio}                                               | 
+ treeview                      |      4 | {bio-phylogeny,bio}                                 | 
  bart-view                     |      3 | {imaging}                                           | 
- biojava-live                  |      3 | {bio-dev}                                           | 
- blasr                         |      3 | {bio,bio-ngs}                                       | 
  elastix                       |      3 | {imaging}                                           | 
- emboss-explorer               |      3 | {bio}                                               | 
  getdata                       |      3 | {bio}                                               | 
- lagan                         |      3 | {bio}                                               | 
  libsbml                       |      3 | {bio-dev}                                           | 
- melting                       |      3 | {cloud,bio}                                         | 
- obitools                      |      3 | {bio}                                               | 
  orthanc-mysql                 |      3 | {imaging}                                           | 
- pbdagcon                      |      3 | {bio}                                               | 
- staden                        |      3 | {bio}                                               | 
- tracetuner                    |      3 | {bio}                                               | 
- beast-mcmc                    |      2 | {bio-phylogeny,bio}                                 | 
- biomaj3-cli                   |      2 | {cloud}                                             | 
- bitseq                        |      2 | {bio}                                               | 
- brig                          |      2 | {bio}                                               | 
- canu                          |      2 | {bio}                                               | 
- embassy-domainatrix           |      2 | {cloud,bio}                                         | 
- embassy-domalign              |      2 | {cloud,bio}                                         | 
- embassy-domsearch             |      2 | {bio,cloud}                                         | 
- gatb-core                     |      2 | {bio}                                               | 
- ghmm                          |      2 | {bio}                                               | 
- jellyfish1                    |      2 | {bio}                                               | 
- lamarc                        |      2 | {bio}                                               | 
- librdp-taxonomy-tree-java     |      2 | {bio-dev}                                           | 
- mhap                          |      2 | {bio,bio-ngs}                                       | 
+ runcircos-gui                 |      3 | {bio}                                               | 
+ stacks                        |      3 | {bio}                                               | 
+ biojava-live                  |      2 | {bio-dev}                                           | 
+ blasr                         |      2 | {bio,bio-ngs}                                       | 
+ emboss-explorer               |      2 | {bio}                                               | 
+ lagan                         |      2 | {bio}                                               | 
+ melting                       |      2 | {cloud,bio}                                         | 
+ ngs-sdk                       |      2 | {bio-dev}                                           | 
  nipype                        |      2 | {imaging-dev,imaging}                               | 
+ obitools                      |      2 | {bio}                                               | 
  orthanc-gdcm                  |      2 | {imaging}                                           | 
- phast                         |      2 | {bio}                                               | 
- phyutility                    |      2 | {bio,cloud}                                         | 
- piler                         |      2 | {bio}                                               | 
+ pbdagcon                      |      2 | {bio}                                               | 
  pymia                         |      2 | {imaging-dev}                                       | 
- rdp-classifier                |      2 | {bio}                                               | 
- saint                         |      2 | {bio}                                               | 
- samblaster                    |      2 | {covid-19,bio}                                      | 
- sibsim4                       |      2 | {cloud,bio}                                         | 
- spread-phy                    |      2 | {bio,bio-phylogeny}                                 | 
- anfo                          |      1 | {bio,cloud}                                         | 
- arden                         |      1 | {cloud,bio}                                         | 
- assemblytics                  |      1 | {bio}                                               | 
- bio-tradis                    |      1 | {bio-dev,bio}                                       | 
+ staden                        |      2 | {bio}                                               | 
+ tracetuner                    |      2 | {bio}                                               | 
+ beast-mcmc                    |      1 | {bio-phylogeny,bio}                                 | 
+ biomaj3-cli                   |      1 | {cloud}                                             | 
+ bitseq                        |      1 | {bio}                                               | 
  blimps                        |      1 | {bio}                                               | 
+ brig                          |      1 | {bio}                                               | 
+ canu                          |      1 | {bio}                                               | 
  cat-bat                       |      1 | {bio,covid-19}                                      | 
- clonalframeml                 |      1 | {covid-19,bio}                                      | 
- clonalorigin                  |      1 | {bio}                                               | 
  cufflinks                     |      1 | {cloud,bio}                                         | 
- delly                         |      1 | {bio,covid-19}                                      | 
- ecopcr                        |      1 | {bio}                                               | 
- estscan                       |      1 | {bio}                                               | 
- fastml                        |      1 | {bio}                                               | 
- fsm-lite                      |      1 | {bio}                                               | 
+ embassy-domainatrix           |      1 | {cloud,bio}                                         | 
+ embassy-domalign              |      1 | {cloud,bio}                                         | 
+ embassy-domsearch             |      1 | {bio,cloud}                                         | 
+ gatb-core                     |      1 | {bio}                                               | 
+ ghmm                          |      1 | {bio}                                               | 
  gifticlib                     |      1 | {imaging-dev}                                       | 
- hinge                         |      1 | {bio}                                               | 
- ipig                          |      1 | {bio}                                               | 
- jmodeltest                    |      1 | {bio-phylogeny,bio}                                 | 
- libncl                        |      1 | {bio}                                               | 
- libpal-java                   |      1 | {bio-dev}                                           | 
+ jellyfish1                    |      1 | {bio}                                               | 
+ lamarc                        |      1 | {bio}                                               | 
+ librdp-taxonomy-tree-java     |      1 | {bio-dev}                                           | 
  libvistaio                    |      1 | {imaging-dev}                                       | 
- logol                         |      1 | {bio}                                               | 
- mauve-aligner                 |      1 | {bio}                                               | 
- metaphlan2                    |      1 | {bio}                                               | 
- microbegps                    |      1 | {bio}                                               | 
+ mhap                          |      1 | {bio,bio-ngs}                                       | 
  orthanc-python                |      1 | {covid-19}                                          | 
  papyrus                       |      1 | {imaging-dev}                                       | 
- paraclu                       |      1 | {cloud,bio}                                         | 
- perm                          |      1 | {cloud,bio}                                         | 
- placnet                       |      1 | {bio}                                               | 
- plasmidseeker                 |      1 | {bio}                                               | 
- prime-phylo                   |      1 | {cloud,bio}                                         | 
- proalign                      |      1 | {bio,bio-phylogeny}                                 | 
- pscan-chip                    |      1 | {bio}                                               | 
- qcumber                       |      1 | {bio}                                               | 
- quorum                        |      1 | {bio}                                               | 
- rambo-k                       |      1 | {bio}                                               | 
- rdp-alignment                 |      1 | {bio}                                               | 
- rtax                          |      1 | {cloud,bio}                                         | 
+ phast                         |      1 | {bio}                                               | 
+ phyutility                    |      1 | {bio,cloud}                                         | 
+ piler                         |      1 | {bio}                                               | 
+ rdp-classifier                |      1 | {bio}                                               | 
+ saint                         |      1 | {bio}                                               | 
  salmon                        |      1 | {bio,covid-19}                                      | 
+ samblaster                    |      1 | {covid-19,bio}                                      | 
  samtools-legacy               |      1 | {bio-dev}                                           | 
- segemehl                      |      1 | {bio}                                               | 
- sga                           |      1 | {bio}                                               | 
+ sibsim4                       |      1 | {cloud,bio}                                         | 
  sift                          |      1 | {bio}                                               | 
- soapaligner                   |      1 | {bio}                                               | 
- soapsnp                       |      1 | {bio}                                               | 
- spaced                        |      1 | {bio}                                               | 
- sprai                         |      1 | {bio}                                               | 
- suitename                     |      1 | {bio}                                               | 
- surankco                      |      1 | {bio}                                               | 
- tvc                           |      1 | {bio}                                               | 
- yaha                          |      1 | {bio}                                               | 
- zalign                        |      1 | {cloud,bio}                                         | 
+ spread-phy                    |      1 | {bio,bio-phylogeny}                                 | 
  acedb                         |      0 | {bio,cloud}                                         | 
+ anfo                          |      0 | {bio,cloud}                                         | 
+ arden                         |      0 | {cloud,bio}                                         | 
+ assemblytics                  |      0 | {bio}                                               | 
  atropos                       |      0 | {bio}                                               | 
  bambamc                       |      0 | {bio-dev}                                           | 
  bamkit                        |      0 | {bio,covid-19}                                      | 
  bbmap                         |      0 | {bio,covid-19}                                      | 
  biojava4-live                 |      0 | {bio-dev}                                           | 
  biosyntax                     |      0 | {bio}                                               | 
+ bio-tradis                    |      0 | {bio-dev,bio}                                       | 
  bmtk                          |      0 | {psychology}                                        | 
  bustools                      |      0 | {bio,covid-19}                                      | 
  camp                          |      0 | {imaging-dev}                                       | 
+ clonalframeml                 |      0 | {covid-19,bio}                                      | 
+ clonalorigin                  |      0 | {bio}                                               | 
  ctn                           |      0 | {imaging-dev}                                       | 
+ delly                         |      0 | {bio,covid-19}                                      | 
  dextractor                    |      0 | {bio,covid-19}                                      | 
+ ecopcr                        |      0 | {bio}                                               | 
  eegdev                        |      0 | {imaging-dev}                                       | 
  emmax                         |      0 | {bio}                                               | 
+ estscan                       |      0 | {bio}                                               | 
+ fastml                        |      0 | {bio}                                               | 
  fis-gtm                       |      0 | {his}                                               | 
+ fsm-lite                      |      0 | {bio}                                               | 
  gatb-core                     |      0 | {bio-dev}                                           | 
+ hinge                         |      0 | {bio}                                               | 
  htscodecs                     |      0 | {covid-19,bio-dev}                                  | 
  intake                        |      0 | {bio-dev,bio}                                       | 
+ ipig                          |      0 | {bio}                                               | 
+ jmodeltest                    |      0 | {bio-phylogeny,bio}                                 | 
  kmerresistance                |      0 | {bio}                                               | 
  libbigwig                     |      0 | {bio-dev}                                           | 
  libbiod                       |      0 | {bio-dev}                                           | 
@@ -184,15 +155,21 @@ Last-Update: Fri, 16 Jul 2021 01:42:04 +0000
  libmialm                      |      0 | {imaging-dev}                                       | 
  libmuscle                     |      0 | {bio-dev}                                           | 
  libncl                        |      0 | {bio-dev}                                           | 
+ libncl                        |      0 | {bio}                                               | 
+ libpal-java                   |      0 | {bio-dev}                                           | 
  libpsortb                     |      0 | {bio-dev}                                           | 
  libqes                        |      0 | {bio-dev}                                           | 
  libseqlib                     |      0 | {bio-dev}                                           | 
  libstatgen                    |      0 | {bio-dev}                                           | 
  libxdf                        |      0 | {imaging-dev}                                       | 
+ logol                         |      0 | {bio}                                               | 
+ mauve-aligner                 |      0 | {bio}                                               | 
+ metaphlan2                    |      0 | {bio}                                               | 
  metastudent-data              |      0 | {bio}                                               | 
  metastudent-data-2            |      0 | {bio}                                               | 
  mia                           |      0 | {imaging-dev}                                       | 
  miaviewit                     |      0 | {imaging-dev}                                       | 
+ microbegps                    |      0 | {bio}                                               | 
  milib                         |      0 | {bio-dev,covid-19}                                  | 
  nanosv                        |      0 | {covid-19,bio}                                      | 
  ncbi-vdb                      |      0 | {bio-dev}                                           | 
@@ -200,39 +177,62 @@ Last-Update: Fri, 16 Jul 2021 01:42:04 +0000
  opencfu                       |      0 | {laboratory}                                        | 
  opensurgsim                   |      0 | {imaging-dev}                                       | 
  orthanc-imagej                |      0 | {imaging}                                           | 
+ paraclu                       |      0 | {cloud,bio}                                         | 
  parallel-fastq-dump           |      0 | {covid-19}                                          | 
  pbcopper                      |      0 | {bio-dev}                                           | 
  pbseqlib                      |      0 | {bio-dev}                                           | 
+ perm                          |      0 | {cloud,bio}                                         | 
  pigx-rnaseq                   |      0 | {covid-19,bio}                                      | 
  pilercr                       |      0 | {bio}                                               | 
  pique                         |      0 | {bio}                                               | 
+ placnet                       |      0 | {bio}                                               | 
  plasmidid                     |      0 | {covid-19,bio}                                      | 
+ plasmidseeker                 |      0 | {bio}                                               | 
  pplacer                       |      0 | {bio-phylogeny,covid-19,bio}                        | 
+ prime-phylo                   |      0 | {cloud,bio}                                         | 
+ proalign                      |      0 | {bio,bio-phylogeny}                                 | 
+ pscan-chip                    |      0 | {bio}                                               | 
  python-bcbio-gff              |      0 | {bio-dev}                                           | 
  python-seqcluster             |      0 | {bio-dev,covid-19}                                  | 
  python-wdlparse               |      0 | {bio-dev}                                           | 
  q2-sample-classifier          |      0 | {bio-dev,bio}                                       | 
+ qcumber                       |      0 | {bio}                                               | 
+ quorum                        |      0 | {bio}                                               | 
+ rambo-k                       |      0 | {bio}                                               | 
+ rdp-alignment                 |      0 | {bio}                                               | 
  resfinder-db                  |      0 | {bio}                                               | 
+ rtax                          |      0 | {cloud,bio}                                         | 
  sambamba                      |      0 | {bio}                                               | 
  sbmltoolbox                   |      0 | {bio-dev}                                           | 
+ segemehl                      |      0 | {bio}                                               | 
  seq-gen                       |      0 | {bio}                                               | 
+ sga                           |      0 | {bio}                                               | 
  shovill                       |      0 | {bio,covid-19}                                      | 
  simpleitk                     |      0 | {imaging-dev}                                       | 
  simrisc                       |      0 | {oncology}                                          | 
  skesa                         |      0 | {bio}                                               | 
  skewer                        |      0 | {bio}                                               | 
  smrtanalysis                  |      0 | {bio,covid-19}                                      | 
+ soapaligner                   |      0 | {bio}                                               | 
+ soapsnp                       |      0 | {bio}                                               | 
+ spaced                        |      0 | {bio}                                               | 
  spaln                         |      0 | {covid-19,bio}                                      | 
+ sprai                         |      0 | {bio}                                               | 
  srf                           |      0 | {bio-dev}                                           | 
+ suitename                     |      0 | {bio}                                               | 
+ surankco                      |      0 | {bio}                                               | 
  svim                          |      0 | {bio}                                               | 
  thesias                       |      0 | {bio,covid-19}                                      | 
  tophat-recondition            |      0 | {bio,covid-19}                                      | 
  trace2dbest                   |      0 | {bio}                                               | 
+ tvc                           |      0 | {bio}                                               | 
  varna                         |      0 | {bio}                                               | 
  varscan                       |      0 | {covid-19,bio}                                      | 
  vienna-rna                    |      0 | {covid-19,bio}                                      | 
  xdffileio                     |      0 | {imaging-dev}                                       | 
+ yaha                          |      0 | {bio}                                               | 
  yanagiba                      |      0 | {bio,covid-19}                                      | 
+ zalign                        |      0 | {cloud,bio}                                         | 
  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/e0e332acd4b2a58bfc557082ffff143d2fa6a3fc

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