replace run_cmd with run_shell_cmd in custom easyblock for Xmipp (xmipp.py)

[branfosj]

(created using eb --new-pr)

• No use of EB_Xmipp in easyconfigs or blocks

[branfosj]

Test report by @branfosj

Overview of tested easyconfigs (in order)

• SUCCESS Xmipp-3.22.07-Helios-foss-2022a.eb
• SUCCESS Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb

Build succeeded for 2 out of 2 (2 easyconfigs in total)
bear-pg0105u03a - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/62964649658dd0cece44abcdb39719ae for a full test report.

[boegel]

lgtm

[boegel]

@boegelbot please test @ jsc-zen3
EB_BRANCH="5.0.x"
EB_ARGS="Xmipp-3.22.07-Helios-foss-2022a.eb --installpath /tmp/$USER/pr3092"

[boegelbot]

@boegel: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ "5.0.x" != 'develop' ]]; then EB_BRANCH="5.0.x" ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/"5.0.x" source init_env_easybuild_develop.sh; fi; EB_PR=3092 EB_ARGS="Xmipp-3.22.07-Helios-foss-2022a.eb --installpath /tmp/$USER/pr3092" EB_REPO=easybuild-easyblocks EB_BRANCH="5.0.x" /opt/software/slurm/bin/sbatch --job-name test_PR_3092 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

• exit code: 0
• output:

Submitted batch job 3507

Test results coming soon (I hope)...

- notification for comment with ID 1915105059 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

[boegelbot]

Test report by @boegelbot

Overview of tested easyconfigs (in order)

• SUCCESS Xmipp-3.22.07-Helios-foss-2022a.eb

Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen3c1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.3, x86_64, AMD EPYC-Milan Processor (zen3), Python 3.9.18
See https://gist.github.com/boegelbot/99a58a9e95926e1459503930b756221f for a full test report.