planemo dependency_script can loose current directory #404
Description
...
<action type="shell_command">cd htslib-1.2.1 && make bgzip tabix</action>
<action type="move_file">
<source>htslib-1.2.1/bgzip</source>
<destination>$INSTALL_DIR/bin</destination>
</action>
<action type="move_file">
<source>htslib-1.2.1/tabix</source>
<destination>$INSTALL_DIR/bin</destination>
</action>
...When run via Galaxy, <action type="shell_command">cd htslib-1.2.1 && make bgzip tabix</action> has no lasting change on the current directory.
Currently via planemo dependency_script use of cd htslib-1.2.1 is never reverted (so the later steps break).
Workaround:
<action type="shell_command">cd htslib-1.2.1 && make bgzip tabix && cd ..</action>Probably the simplest fix is to append cd $dep_install_tmp to the conversion of any <action type="shell_command"> step?