Clinical-Genomics / microSALT

Microbial Sequence Analysis and Loci-based Typing pipeline for use on NGS WGS data.

GNU General Public License v3.0

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Fixed conda installation #166

Closed talnor closed 7 months ago

talnor commented 8 months ago

Description

added environment.yml for installation script.

Source activate is no longer supported on the servers. Will be fixed in servers repo.

Primary function of PR

[x] Hotfix
[ ] 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

Tests

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.

Test routine to verify the stability of the PR:

_yes | bash <(curl https://raw.githubusercontent.com/Clinical-Genomics/microSALT/fix_installation_conda/install.sh) fix_installation_conda microSALT_
- [x] Ensure that there are no error messages
- [x] and that microSALT is installed in the conda environment
conda env create -n S_microSALT -f https://raw.githubusercontent.com/Clinical-Genomics/microSALT/fix_installation_conda/environment.yml
- [x] Ensure that there are no errors

Test results

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

no errors.

Sign-offs

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