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add software required for 'mag' Nextflow pipeline to EESSI 2021.12 #202

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smoretti wants to merge 9 commits into from
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add software required for 'mag' Nextflow pipeline to EESSI 2021.12 #202

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d31643a
Draft of the pipeline installation in EESSI
smoretti Nov 10, 2022
21b6980
Update the Nextflow-pipeline PR
smoretti Nov 10, 2022
7eeacc9
Update Nextflow pipeline name
smoretti Nov 11, 2022
e0ec46c
Add new PRs
smoretti Nov 11, 2022
fb934d4
Fix the list of PR to only the bundle and the MetaBAT fix
smoretti Nov 15, 2022
85ea3cd
Install R-4.1.0-foss-2021a.eb first for the Nextflow mag pipeline to …
smoretti Dec 14, 2022
aeab8e0
Use the last R-4.1.0-foss-2021a.eb PR to use SYSTEM template constant…
smoretti Dec 14, 2022
6243c5d
Add R 4.1.0 as a separate PR in the EESSI pilot script
smoretti Dec 14, 2022
513c896
Move R 4.1.0 in a separate PR
smoretti Dec 14, 2022
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6 changes: 6 additions & 0 deletions EESSI-pilot-install-software.sh
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Expand Up @@ -362,6 +362,12 @@ fail_msg="Installation of Nextflow failed, that's unexpected..."
$EB -r --from-pr 16531 Nextflow-22.10.1.eb
check_exit_code $? "${ok_msg}" "${fail_msg}"

echo ">> Installing requirements for the Nextflow mag 20221110 pipeline..."
ok_msg="The full Nextflow pipeline is installed, the work must flow..."
fail_msg="Installation of the Nextflow pipeline failed, that's unexpected..."
$EB --from-pr 16624 MetaBAT-2.15-gompi-2021a.eb -r && $EB --from-pr 16613 -r
check_exit_code $? "${ok_msg}" "${fail_msg}"

### add packages here

echo ">> Creating/updating Lmod cache..."
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4 changes: 4 additions & 0 deletions eessi-2021.12.yml
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Expand Up @@ -57,3 +57,7 @@ software:
toolchains:
SYSTEM:
versions: '22.10.1'
nf-core-mag:
toolchains:
foss-2021a:
versions: '20221110'