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

Andreas Tille gitlab at salsa.debian.org
Wed May 20 14:45:44 BST 2020



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


Commits:
8f7d3b8c by Andreas Tille at 2020-05-20T13:45:36+00:00
automatic update

- - - - -


2 changed files:

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


Changes:

=====================================
debian-med-tests.txt
=====================================
@@ -1,41 +1,41 @@
-Last-Update: Wed, 20 May 2020 01:42:03 +0000
+Last-Update: Wed, 20 May 2020 13:42:04 +0000
 
  Source                        | Vote   |     Tasks                                           |                                 Tags                                 
 -------------------------------+--------+-----------------------------------------------------+----------------------------------------------------------------------
- dcmtk                         |    190 | {imaging,covid-19}                                  | 
- orthanc                       |     99 | {imaging,covid-19,practice}                         | 
- gdcm                          |     54 | {imaging-dev}                                       | 
- orthanc-wsi                   |     48 | {oncology,practice,laboratory,his,imaging,covid-19} | 
+ dcmtk                         |    191 | {covid-19,imaging}                                  | 
+ orthanc                       |    100 | {practice,imaging,covid-19}                         | 
+ gdcm                          |     52 | {imaging-dev}                                       | 
+ orthanc-wsi                   |     48 | {imaging,oncology,his,practice,covid-19,laboratory} | 
+ dicom3tools                   |     31 | {imaging}                                           | 
  htsjdk                        |     31 | {bio-dev}                                           | 
  dicomscope                    |     30 | {imaging}                                           | 
- dicom3tools                   |     29 | {imaging}                                           | 
- dcm2niix                      |     22 | {imaging}                                           | 
- gdcm                          |     18 | {covid-19,imaging}                                  | 
- gnumed-server                 |     17 | {practice,covid-19}                                 | 
- minc-tools                    |     17 | {imaging}                                           | 
+ dcm2niix                      |     23 | {imaging}                                           | 
+ gdcm                          |     19 | {imaging,covid-19}                                  | 
+ minc-tools                    |     19 | {imaging}                                           | 
+ pixelmed                      |     18 | {imaging}                                           | 
+ gnumed-server                 |     17 | {covid-19,practice}                                 | 
  insighttoolkit4               |     16 | {imaging-dev}                                       | 
- pixelmed                      |     16 | {imaging}                                           | 
  invesalius                    |     15 | {imaging}                                           | 
- plastimatch                   |     14 | {imaging}                                           | 
- adun.app                      |     13 | {bio}                                               | 
+ plastimatch                   |     15 | {imaging}                                           | 
+ adun.app                      |     14 | {bio}                                               | 
+ openslide                     |     14 | {imaging}                                           | 
+ vtk-dicom                     |     14 | {imaging}                                           | 
+ king                          |     13 | {typesetting,imaging}                               | 
  ngs-sdk                       |     13 | {bio-dev}                                           | 
- openslide                     |     13 | {imaging}                                           | 
  stacks                        |     13 | {bio}                                               | 
- vtk-dicom                     |     13 | {imaging}                                           | 
- king                          |     12 | {typesetting,imaging}                               | 
- biosig4c++                    |     10 | {imaging,physics}                                   | 
+ biosig4c++                    |     11 | {physics,imaging}                                   | 
  gdcm                          |     10 | {imaging-dev}                                       | 
  librg-utils-perl              |     10 | {bio}                                               | 
+ ngs-sdk                       |     10 | {bio-dev}                                           | 
  biojava-live                  |      9 | {bio-dev}                                           | 
  jebl2                         |      9 | {bio-dev}                                           | 
- ngs-sdk                       |      9 | {bio-dev}                                           | 
  obitools                      |      9 | {bio}                                               | 
  ea-utils                      |      8 | {bio}                                               | 
  fastlink                      |      8 | {bio,cloud}                                         | 
  paml                          |      8 | {bio}                                               | 
  alter-sequence-alignment      |      7 | {bio}                                               | 
- ampliconnoise                 |      7 | {cloud,bio}                                         | 
- arden                         |      7 | {bio,cloud}                                         | 
+ ampliconnoise                 |      7 | {bio,cloud}                                         | 
+ arden                         |      7 | {cloud,bio}                                         | 
  indelible                     |      7 | {bio}                                               | 
  maqview                       |      7 | {bio}                                               | 
  melting                       |      7 | {bio,cloud}                                         | 
@@ -45,51 +45,51 @@ Last-Update: Wed, 20 May 2020 01:42:03 +0000
  orthanc-webviewer             |      7 | {imaging}                                           | 
  piler                         |      7 | {bio}                                               | 
  staden                        |      7 | {bio}                                               | 
- abacas                        |      6 | {bio,covid-19}                                      | 
+ abacas                        |      6 | {covid-19,bio}                                      | 
  anfo                          |      6 | {cloud,bio}                                         | 
  biomaj3-cli                   |      6 | {cloud}                                             | 
  bio-rainbow                   |      6 | {bio}                                               | 
- bio-tradis                    |      6 | {bio-dev,bio}                                       | 
+ bio-tradis                    |      6 | {bio,bio-dev}                                       | 
  bppsuite                      |      6 | {bio}                                               | 
  cgview                        |      6 | {bio}                                               | 
  dazzdb                        |      6 | {bio}                                               | 
  edtsurf                       |      6 | {bio}                                               | 
  embassy-domainatrix           |      6 | {cloud,bio}                                         | 
- embassy-domalign              |      6 | {bio,cloud}                                         | 
+ embassy-domalign              |      6 | {cloud,bio}                                         | 
  libminc                       |      6 | {imaging-dev}                                       | 
- nutsqlite                     |      6 | {tools}                                             | 
  orthanc-dicomweb              |      6 | {imaging,covid-19}                                  | 
  orthanc-mysql                 |      6 | {imaging}                                           | 
  psychopy                      |      6 | {psychology}                                        | 
  pymia                         |      6 | {imaging-dev}                                       | 
  radiant                       |      6 | {bio}                                               | 
  saint                         |      6 | {bio}                                               | 
- salmon                        |      6 | {bio,covid-19}                                      | 
+ salmon                        |      6 | {covid-19,bio}                                      | 
  seer                          |      6 | {bio}                                               | 
- sibsim4                       |      6 | {cloud,bio}                                         | 
- sigma-align                   |      6 | {cloud,bio,bio-phylogeny}                           | 
+ sibsim4                       |      6 | {bio,cloud}                                         | 
+ sigma-align                   |      6 | {bio-phylogeny,bio,cloud}                           | 
  transrate-tools               |      6 | {bio}                                               | 
  transtermhp                   |      6 | {bio}                                               | 
  bart-view                     |      5 | {imaging}                                           | 
  beast-mcmc                    |      5 | {bio,bio-phylogeny}                                 | 
  bitseq                        |      5 | {bio}                                               | 
  cluster3                      |      5 | {bio}                                               | 
- daligner                      |      5 | {bio-ngs,bio}                                       | 
+ daligner                      |      5 | {bio,bio-ngs}                                       | 
  ecopcr                        |      5 | {bio}                                               | 
- embassy-domsearch             |      5 | {bio,cloud}                                         | 
- gasic                         |      5 | {cloud,bio}                                         | 
+ embassy-domsearch             |      5 | {cloud,bio}                                         | 
+ gasic                         |      5 | {bio,cloud}                                         | 
  gatb-core                     |      5 | {bio}                                               | 
  ipig                          |      5 | {bio}                                               | 
  jellyfish1                    |      5 | {bio}                                               | 
  king-probe                    |      5 | {bio}                                               | 
  lagan                         |      5 | {bio}                                               | 
- mapsembler2                   |      5 | {cloud,bio}                                         | 
+ mapsembler2                   |      5 | {bio,cloud}                                         | 
  mrs                           |      5 | {bio}                                               | 
  neobio                        |      5 | {cloud,bio}                                         | 
+ nutsqlite                     |      5 | {tools}                                             | 
  orthanc-postgresql            |      5 | {imaging}                                           | 
- paraclu                       |      5 | {cloud,bio}                                         | 
+ paraclu                       |      5 | {bio,cloud}                                         | 
  phast                         |      5 | {bio}                                               | 
- phyutility                    |      5 | {cloud,bio}                                         | 
+ phyutility                    |      5 | {bio,cloud}                                         | 
  predictprotein                |      5 | {bio}                                               | 
  probabel                      |      5 | {cloud,bio}                                         | 
  pscan-tfbs                    |      5 | {bio}                                               | 
@@ -97,8 +97,8 @@ Last-Update: Wed, 20 May 2020 01:42:03 +0000
  seqtools                      |      5 | {bio}                                               | 
  sickle                        |      5 | {bio}                                               | 
  squizz                        |      5 | {cloud,bio}                                         | 
- treeview                      |      5 | {bio,bio-phylogeny}                                 | 
- zalign                        |      5 | {bio,cloud}                                         | 
+ treeview                      |      5 | {bio-phylogeny,bio}                                 | 
+ zalign                        |      5 | {cloud,bio}                                         | 
  assemblytics                  |      4 | {bio}                                               | 
  baitfisher                    |      4 | {bio}                                               | 
  bandage                       |      4 | {bio}                                               | 
@@ -117,7 +117,7 @@ Last-Update: Wed, 20 May 2020 01:42:03 +0000
  fsm-lite                      |      4 | {bio}                                               | 
  harvest-tools                 |      4 | {bio}                                               | 
  jaligner                      |      4 | {bio}                                               | 
- jmodeltest                    |      4 | {bio-phylogeny,bio}                                 | 
+ jmodeltest                    |      4 | {bio,bio-phylogeny}                                 | 
  libdivsufsort                 |      4 | {bio-dev}                                           | 
  libgff                        |      4 | {bio-dev}                                           | 
  libncl                        |      4 | {bio}                                               | 
@@ -129,7 +129,7 @@ Last-Update: Wed, 20 May 2020 01:42:03 +0000
  phybin                        |      4 | {bio}                                               | 
  placnet                       |      4 | {bio}                                               | 
  poretools                     |      4 | {bio}                                               | 
- prime-phylo                   |      4 | {cloud,bio}                                         | 
+ prime-phylo                   |      4 | {bio,cloud}                                         | 
  proalign                      |      4 | {bio,bio-phylogeny}                                 | 
  rambo-k                       |      4 | {bio}                                               | 
  rdp-alignment                 |      4 | {bio}                                               | 
@@ -144,12 +144,12 @@ Last-Update: Wed, 20 May 2020 01:42:03 +0000
  soapaligner                   |      4 | {bio}                                               | 
  soapsnp                       |      4 | {bio}                                               | 
  sprai                         |      4 | {bio}                                               | 
- spread-phy                    |      4 | {bio-phylogeny,bio}                                 | 
+ spread-phy                    |      4 | {bio,bio-phylogeny}                                 | 
  beast2-mcmc                   |      3 | {bio}                                               | 
- blasr                         |      3 | {bio,bio-ngs}                                       | 
+ blasr                         |      3 | {bio-ngs,bio}                                       | 
  canu                          |      3 | {bio}                                               | 
- centrifuge                    |      3 | {covid-19,bio}                                      | 
- cufflinks                     |      3 | {cloud,bio}                                         | 
+ centrifuge                    |      3 | {bio,covid-19}                                      | 
+ cufflinks                     |      3 | {bio,cloud}                                         | 
  delly                         |      3 | {covid-19,bio}                                      | 
  dwgsim                        |      3 | {bio}                                               | 
  elph                          |      3 | {bio}                                               | 
@@ -162,7 +162,7 @@ Last-Update: Wed, 20 May 2020 01:42:03 +0000
  maffilter                     |      3 | {bio}                                               | 
  mauve-aligner                 |      3 | {bio}                                               | 
  mhap                          |      3 | {bio,bio-ngs}                                       | 
- mlv-smile                     |      3 | {bio,cloud}                                         | 
+ mlv-smile                     |      3 | {cloud,bio}                                         | 
  mptp                          |      3 | {bio}                                               | 
  patman                        |      3 | {bio}                                               | 
  phipack                       |      3 | {bio}                                               | 
@@ -174,7 +174,7 @@ Last-Update: Wed, 20 May 2020 01:42:03 +0000
  rdp-classifier                |      3 | {bio}                                               | 
  rtax                          |      3 | {cloud,bio}                                         | 
  scrm                          |      3 | {bio}                                               | 
- seqmagick                     |      3 | {bio,covid-19}                                      | 
+ seqmagick                     |      3 | {covid-19,bio}                                      | 
  seqsero                       |      3 | {bio}                                               | 
  spaced                        |      3 | {bio}                                               | 
  srf                           |      3 | {bio-dev}                                           | 
@@ -198,7 +198,7 @@ Last-Update: Wed, 20 May 2020 01:42:03 +0000
  metaphlan2                    |      2 | {bio}                                               | 
  nanook                        |      2 | {bio}                                               | 
  openslide                     |      2 | {imaging-dev}                                       | 
- oscar                         |      2 | {practice,tools,data}                               | 
+ oscar                         |      2 | {tools,data,practice}                               | 
  pal2nal                       |      2 | {bio}                                               | 
  pbdagcon                      |      2 | {bio}                                               | 
  pilon                         |      2 | {bio}                                               | 
@@ -211,42 +211,42 @@ Last-Update: Wed, 20 May 2020 01:42:03 +0000
  sweed                         |      2 | {bio}                                               | 
  trace2dbest                   |      2 | {bio}                                               | 
  tvc                           |      2 | {bio}                                               | 
- acedb                         |      1 | {cloud,bio}                                         | 
+ acedb                         |      1 | {bio,cloud}                                         | 
  biobambam2                    |      1 | {bio,covid-19,bio-dev}                              | 
  blimps                        |      1 | {bio}                                               | 
+ busco                         |      1 | {bio,covid-19}                                      | 
  embassy-phylip                |      1 | {bio,cloud}                                         | 
  emboss-explorer               |      1 | {bio}                                               | 
  emmax                         |      1 | {bio}                                               | 
  gatb-core                     |      1 | {bio-dev}                                           | 
  libchado-perl                 |      1 | {bio-dev}                                           | 
- libmaus2                      |      1 | {bio-dev,covid-19}                                  | 
+ libmaus2                      |      1 | {covid-19,bio-dev}                                  | 
  libmialm                      |      1 | {imaging-dev}                                       | 
  libsmithwaterman              |      1 | {bio-dev}                                           | 
  libxdf                        |      1 | {imaging-dev}                                       | 
  ncbi-vdb                      |      1 | {bio-dev}                                           | 
  opensurgsim                   |      1 | {imaging-dev}                                       | 
  papyrus                       |      1 | {imaging-dev}                                       | 
- python-py2bit                 |      1 | {bio,bio-dev}                                       | 
+ python-py2bit                 |      1 | {bio-dev,bio}                                       | 
  python-scitrack               |      1 | {covid-19}                                          | 
  relion                        |      1 | {bio}                                               | 
  seqan                         |      1 | {bio-dev}                                           | 
  sift                          |      1 | {bio}                                               | 
  simpleitk                     |      1 | {imaging-dev}                                       | 
  skesa                         |      1 | {bio}                                               | 
- spaln                         |      1 | {covid-19,bio}                                      | 
- varscan                       |      1 | {covid-19,bio}                                      | 
+ spaln                         |      1 | {bio,covid-19}                                      | 
+ varscan                       |      1 | {bio,covid-19}                                      | 
  volpack                       |      1 | {imaging-dev}                                       | 
- augur                         |      0 | {covid-19,bio}                                      | 
+ augur                         |      0 | {bio,covid-19}                                      | 
  bambamc                       |      0 | {bio-dev}                                           | 
  bbmap                         |      0 | {covid-19}                                          | 
  biojava4-live                 |      0 | {bio-dev}                                           | 
  biosig4c++                    |      0 | {physics}                                           | 
  biosyntax                     |      0 | {bio}                                               | 
- busco                         |      0 | {covid-19}                                          | 
  camp                          |      0 | {imaging-dev}                                       | 
  ctn                           |      0 | {imaging-dev}                                       | 
  fis-gtm                       |      0 | {his}                                               | 
- htscodecs                     |      0 | {bio-dev,covid-19}                                  | 
+ htscodecs                     |      0 | {covid-19,bio-dev}                                  | 
  libbigwig                     |      0 | {bio-dev}                                           | 
  libbiod                       |      0 | {bio-dev}                                           | 
  libbioparser-dev              |      0 | {bio-dev}                                           | 
@@ -261,7 +261,7 @@ Last-Update: Wed, 20 May 2020 01:42:03 +0000
  libgenome                     |      0 | {bio-dev}                                           | 
  libgkarrays                   |      0 | {bio-dev}                                           | 
  libhmsbeagle                  |      0 | {bio-dev}                                           | 
- libics                        |      0 | {imaging-dev,covid-19}                              | 
+ libics                        |      0 | {covid-19,imaging-dev}                              | 
  libjloda-java                 |      0 | {bio-dev}                                           | 
  libmems                       |      0 | {bio-dev}                                           | 
  libmuscle                     |      0 | {bio-dev}                                           | 
@@ -281,6 +281,7 @@ Last-Update: Wed, 20 May 2020 01:42:03 +0000
  ngs-sdk                       |      0 | {bio-dev}                                           | 
  opencfu                       |      0 | {laboratory}                                        | 
  orthanc-imagej                |      0 | {imaging}                                           | 
+ parallel-fastq-dump           |      0 | {covid-19}                                          | 
  pbcopper                      |      0 | {bio-dev}                                           | 
  pbseqlib                      |      0 | {bio-dev}                                           | 
  pilercr                       |      0 | {bio}                                               | 
@@ -293,11 +294,10 @@ Last-Update: Wed, 20 May 2020 01:42:03 +0000
  skewer                        |      0 | {bio}                                               | 
  smrtanalysis                  |      0 | {bio,covid-19}                                      | 
  solvate                       |      0 | {bio}                                               | 
- thesias                       |      0 | {bio,covid-19}                                      | 
+ thesias                       |      0 | {covid-19,bio}                                      | 
  varna                         |      0 | {bio}                                               | 
  vtk-dicom                     |      0 | {imaging-dev}                                       | 
  wtdbg2                        |      0 | {covid-19}                                          | 
- bustools                      |     -1 | {bio,covid-19}                                      | 
- parallel-fastq-dump           |     -1 | {covid-19}                                          | 
+ bustools                      |     -1 | {covid-19,bio}                                      | 
 (326 rows)
 


=====================================
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/8f7d3b8cbf64e837b0310dcba8df57e379fe5d95

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View it on GitLab: https://salsa.debian.org/med-team/community/helper-scripts/-/commit/8f7d3b8cbf64e837b0310dcba8df57e379fe5d95
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