I originally posted this question <https://biostar.usegalaxy.org/p/9401/>
on the Galaxy Biostars, but later realized that galaxy-dev is probably more
appropriate. So, here it goes.

I'm trying to automate the installation of a tool's dependency with a tool
dependency definition repository. During the package installation process,
after moving the contents of a downloaded archive to the installation
directory (*i.e.* $INSTALL_DIR), I simply want to change to that target
directory away from the initial temporary working directory.

However, I can't seem to change directory, either with a change_directory
action or a cd shell_command action. Running pwd before and after
attempting to change directory confirms this (see attached for installation
log). I even made sure that $INSTALL_DIR is different from my initial
working directory.

Best regards,
Bruno
#############################################
pwd
STDOUT
/home/galaxy/galaxy_dist/database/tmp/tmp-toolshed-mtdIAQaet/ensembl-tools-release-77
#############################################

#############################################
pwd
STDERR

#############################################

#############################################
echo 
/home/galaxy/tool_dependencies/ensembl_vep/77/bgrande/ensembl_vep_installer/ca420305feb8
STDOUT
/home/galaxy/tool_dependencies/ensembl_vep/77/bgrande/ensembl_vep_installer/ca420305feb8
#############################################

#############################################
echo 
/home/galaxy/tool_dependencies/ensembl_vep/77/bgrande/ensembl_vep_installer/ca420305feb8
STDERR

#############################################

#############################################
cd 
/home/galaxy/tool_dependencies/ensembl_vep/77/bgrande/ensembl_vep_installer/ca420305feb8
STDOUT

#############################################

#############################################
cd 
/home/galaxy/tool_dependencies/ensembl_vep/77/bgrande/ensembl_vep_installer/ca420305feb8
STDERR

#############################################

#############################################
pwd
STDOUT
/home/galaxy/galaxy_dist/database/tmp/tmp-toolshed-mtdIAQaet/ensembl-tools-release-77
#############################################

#############################################
pwd
STDERR

#############################################

#############################################
perl INSTALL.pl --DESTDIR 
/home/galaxy/tool_dependencies/ensembl_vep/77/bgrande/ensembl_vep_installer/ca420305feb8
 --CACHEDIR 
/home/galaxy/tool_dependencies/ensembl_vep/77/bgrande/ensembl_vep_installer/ca420305feb8/.vep
 --SPECIES homo_sapiens --ASSEMBLY GRCh37 --AUTO acf --QUIET
STDOUT

#############################################

#############################################
perl INSTALL.pl --DESTDIR 
/home/galaxy/tool_dependencies/ensembl_vep/77/bgrande/ensembl_vep_installer/ca420305feb8
 --CACHEDIR 
/home/galaxy/tool_dependencies/ensembl_vep/77/bgrande/ensembl_vep_installer/ca420305feb8/.vep
 --SPECIES homo_sapiens --ASSEMBLY GRCh37 --AUTO acf --QUIET
STDERR
Can't open perl script "INSTALL.pl": No such file or directory
############################################
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