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replace run_cmd with run_shell_cmd in custom easyblock for Xmipp (xmipp.py) #3092

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merged 1 commit into from
Jan 29, 2024
Merged

replace run_cmd with run_shell_cmd in custom easyblock for Xmipp (xmipp.py) #3092

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8 changes: 4 additions & 4 deletions easybuild/easyblocks/x/xmipp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@
from easybuild.tools.filetools import apply_regex_substitutions, change_dir
from easybuild.tools.filetools import copy_file, mkdir, remove_file, symlink
from easybuild.tools.modules import get_software_root, get_software_version
from easybuild.tools.run import run_cmd
from easybuild.tools.run import run_shell_cmd
from easybuild.tools.systemtools import get_shared_lib_ext


Expand Down Expand Up @@ -112,7 +112,7 @@ def configure_step(self):
noask,
self.cfg['configopts'],
])
run_cmd(cmd, log_all=True, simple=True)
run_shell_cmd(cmd)

# Parameters to be set in the config file
params = {
Expand Down Expand Up @@ -237,7 +237,7 @@ def build_step(self):
'all',
self.cfg['buildopts'],
])
run_cmd(cmd, log_all=True, simple=True)
run_shell_cmd(cmd)
change_dir(cwd)
xmipp_lib = os.path.join(self.srcdir, 'xmipp', 'lib')
mkdir(xmipp_lib)
Expand Down Expand Up @@ -265,7 +265,7 @@ def install_step(self):
self.installdir,
self.cfg['installopts'],
])
run_cmd(cmd, log_all=True, simple=True)
run_shell_cmd(cmd)

# Remove the bash and fish files. Everything should be in the module
remove_file(os.path.join(self.installdir, 'xmipp.bashrc'))
Expand Down