Hi, Karen. The toolshed has changed a lot recently so if you are not running the latest Galaxy release, try updating? If that doesn't help maybe check with the tool author? Another htseq based wrapper htseq_bams_to_count_matrix which passes tests can be installed via the admin menu from the test toolshed via the admin menu or viewed at https://testtoolshed.g2.bx.psu.edu/view/fubar/htseq_bams_to_count_matrix.
On Tue, Jun 10, 2014 at 6:04 PM, Karen Chait <kch...@techunix.technion.ac.il > wrote: > Hi, > > I am trying to install the tool htseq-count from the tool-shed. I had a > problem in the first installation so I uninstalled the tool and all its > dependencies (numpy, samtools 0.1.19 and pysam) from the ‘manage installed > tool shed repositories) and installed it again but then I get installation > status ‘Installed, missing tool dependencies’ for htseq-count. > > When running this tool I get the error > > Fatal error: The HTSeq python package is not properly installed, contact > Galaxy administrators > > The path set in universe_wsgi.ini: > > tool_dependency_dir = /home/galaxy/galaxy-dist/tool_deps > > > > in the installation log > htseq/0.6.1/lparsons/htseq_count/d5edaf8dc974/INSTALLATION.log I get the > error: > > Setup script for HTSeq: Failed to import 'numpy'. > > Please install numpy and then try again to install HTSeq. > > > > I reinstalled numpy but that did not help. > > How should I continue? > > Thanks, > > Karen > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ >
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
