Hi all,

Installing htseq-count with dependencies fails on my system: htseq-count installs four dependencies (numpy, picard, samtools, htseq) , of which one fails (htseq), strangely enough.

The error is:

error: can't create or remove files in install directory

The following error occurred while trying to add or remove files in the
installation directory:

[Errno 2] No such file or directory: '/apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/test-easy-install-856.pth'

The installation directory you specified (via --install-dir, --prefix, or
the distutils default setting) was:


This directory does not currently exist. Please create it and try again, or
choose a different installation directory (using the -d or --install-dir

The /apps directory is completely owned by Galaxy. I tried to create that missing directory (reported above), but got a little stuck, since uninstalling the dependency removed that directory again.

The tool created the folder /apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e
with contents:


Next I looked to the tool_dependency.xml, but with my limited experience did not see something obvious.

Thanks for any hint, (prefer to get the installation working from the toolshed)


Joachim Jacob

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)

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