Fix cli pip install

[henrikstranneheim]

Description

Added

Changed

Fixed

How to prepare for test

• Ssh to relevant server (depending on type of change)
• Use stage: us
• Paxa the environment: paxa
• Install on stage (example for Hasta):

  bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_crunchy -t crunchy -b fix-cli-pip-install

How to test

• Do ...

Expected test outcome

• Check that ...
• Take a screenshot and attach or copy/paste the output.

Review

• Tests executed by
• "Merge and deploy" approved by
  Thanks for filling in who performed the code review and the test!

This version is a

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

• Document in ...
• Deploy this branch on ...
• Inform to ...

[sonarcloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 76.95%. Comparing base (aed91f3) to head (b9045a6).
Report is 4 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master      #34   +/-   ##
=======================================
  Coverage   76.95%   76.95%           
=======================================
  Files          16       16           
  Lines         590      590           
=======================================
  Hits          454      454           
  Misses        136      136           

Flag	Coverage Δ
unittests	76.95% <ø> (ø)

Flags with carried forward coverage won't be shown. Click here to find out more.

[henrikstranneheim]

PIP install Crunchy, 👍

henrik.stranneheim@hasta:~] [S_base] $ conda  activate S_crunchy
[henrik.stranneheim@hasta:~] [S_crunchy] $  crunchy
Usage: crunchy [OPTIONS] COMMAND [ARGS]...

  Base command for crunchy

                .---. .---.
               :     : o   :    me want cookie!
           _..-:   o :     :-.._    /
       .-''  '  `---' `---' "   ``-.
     .'   "   '  "  .    "  . '  "  `.
    :   '.---.,,.,...,.,.,.,..---.  ' ;
    `. " `.                     .' " .'
     `.  '`.                   .' ' .'
      `.    `-._           _.-' "  .'  .----.
        `. "    '"--...--"'  . ' .'  .'  o   `.
        .'`-._'    " .     " _.-'`. :       o  :
      .'      ```--.....--'''    ' `:_ o       :
    .'    "     '         "     "   ; `.;";";";'
   ;         '       "       '     . ; .' ; ; ;
  ;     '         '       '   "    .'      .-'
  '  "     "   '      "           "    _.-'

Options:
  --spring-binary TEXT            Path to spring binary  [default: spring]
  --samtools-binary TEXT          Path to spring binary  [default: samtools]
  -t, --threads INTEGER           Number of threads to use for spring
                                  compression  [default: 8]
  --version                       Show the version and exit.
  -r, --reference TEXT            Path to reference genome
  --log-level [DEBUG|INFO|WARNING]
                                  Choose what log messages to show
  --tmp-dir TEXT                  If specific temp dir should be used
  --help                          Show this message and exit.

Commands:
  auto        Run whole pipeline by compressing, comparing and deleting...
  checksum    Generate the checksum for a file.
  compare     Compare two files by generating checksums.
  compress    Compress genomic files.
  decompress  Decompress genomic files

[ChrOertlin]

💯

[henrikstranneheim]

Nothing to deploy