Fix dependencies

[talnor]

Description

Some of microSALTs dependencies are no longer available and other dependencies causes the installation to fail.

The features of this PR primarily concerns bioinformaticians/internals

Summary of the changes made:

• Update version of samtools
• Update version of a few other tools (see install.sh)
• Update click
• Set versions for requirements-dev.txt

If not self-evident, mention what prompted the change. Unable to run microSALT installation

Primary function of PR

• [ ] Hotfix
• [x] Patch
• [ ] Minor functionality improvement
• [ ] New type of analysis
• [ ] Backward-breaking functionality improvement
• [ ] This change requires internal documents to be updated
• [ ] This change requires another repository to be updated

Testing

If the update is a hotfix, it is sufficient to rely on the development testing along with the Travis self-test automatically applied to the PR.

Deploy correct branch on stage:

• _bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-microsalt-stage.sh fix_dependencies_

If starting microSALT with cg:

• us
• paxa -u <user> -s hasta -r cg-stage
• bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-cg-stage.sh master

Test routine to verify the stability of the PR:

• Run microSALT with one of the following commands:
  • microSALT analyse /home/proj/stage/microbial/queries/merrymink.json --input /home/proj/stage/microbial/fastq/merrymink/
  • cg workflow microsalt start merrymink

_Verify that the results for projects MIC3109, MIC4107, MIC4109 & ACC5551 are consistent with the results attached to AMSystem doc 1490, MicrobialWGS.xlsx

Test results

These are the results of the tests, and necessary conclusions, that prove the stability of the PR.

Sign-offs

• [x] Code tested by @talnor
• [x] Approved to run at Clinical-Genomics by @talnor

[talnor]

Reports generated with expected results: 609108_QC_4.txt 609108_Typing_4.txt