Just to confirm, you used automated installation via the admin menu -> search and browse toolsheds -> test toolshed -> etc ?
If you installed manually by downloading and unpacking the archive under your tools/ directory, then yes, there is no automation and you need to install the binary on your path. I believe the documentation explains this - if it's not clear please suggest some revisions ?On Mon, Dec 2, 2013 at 9:18 AM, Karen Miga <khmiga@soe.ucsc.edu> wrote:
Hi Ross,That is listed as "tool_dependency_dir = /mnt/galaxy/tools" in my universe_wsgi.ini file, and that did not contain a clustalw directory either before or after the toolshed install.KarenOn Sun, Dec 1, 2013 at 2:10 PM, Ross <ross.lazarus@gmail.com> wrote:
yes. In universe_wsgi_ini you have a definition for tool_dependency_dir - that's why I wrote: [tool_dependency_directory]/clustalw/2.1/fubar/clustalw/76de6971a0de/ as the path - the funny numbers are the repository revision number - that's where the toolshed installs the binary and the env.sh file needed for the tool to find it.--On Mon, Dec 2, 2013 at 9:08 AM, Karen Miga <khmiga@soe.ucsc.edu> wrote:
Hi Ross,I did not detect any type of auto-install (?) After installing from toolshed I did not find the binary under the /mnt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ (or /mnt/galaxy/tools or /mnt/galaxy/tools/bin for that matter). Am I looking in the wrong place?KarenOn Sun, Dec 1, 2013 at 2:00 PM, Ross <ross.lazarus@gmail.com> wrote:
Hi Karen,Glad to hear it worked for you. It the tool auto-installs correctly, it downloads and unpacks the binary under [tool_dependency_directory]/clustalw/2.1/fubar/clustalw/76de6971a0de/ so the binary you installed manually should not ever be needed by the toolshed version - try moving it off your path - the tool should continue to work correctly? Apologies - I should have suggested removing any manual installations and their corresponding tool_conf.xml entries before using the automated installation - the tool shed installation doesn't prevent you from having 2 versions of the same tool in your tool menu - until those manually installed ones (which may depend on clustalw2 being on the path) are removed?On Mon, Dec 2, 2013 at 8:36 AM, Karen Miga <khmiga@soe.ucsc.edu> wrote:Hi Ross,Thanks for your email. I have clustalw2 working now - I installed the clustal repository (as suggested) from toolshed and then installed the clustalw2 binaries in our mnt/galaxy/tools/bin.Thanks again!KarenOn Wed, Nov 27, 2013 at 12:46 AM, Ross <ross.lazarus@gmail.com> wrote:
Hi, Karen - how did you install clustalw?
If not already done, can you please try installing the clustal repository owned by fubar from the test toolshed through your Galaxy admin interface - search/browse toolsheds? Please let me know how you go and if there's a problem I'll try to fix it for you. I think there's a clustal omega tool too but it's not one of mine. As far as I know my clustal repository should install cleanly on a CloudMan instance.Sorry but we'll have to wait to from someone who knows about HyPhy.
Hello - I am running to errors when trying to run Clustalw and HyPhy on our cloudman instance.(1) Clustalw: The program completes without error and produces an empty file and a log file that states "/bin/sh: 1: clustalw2: not found"Searching around a bit I am not seeing clustalw2 previously installed. I am happy to do it if need be, however, I wanted to check in and see if I am overlooking the directory or an easy fix.If I do need to install clustalw, I would prefer to use clustalw-omega, but was not sure if I needed to script a brand new wrapper or if I could use the previous one that came with galaxy image.(2) HyPhy: The cloud the link was initially broken. I changed it to the correct path:sudo ln -sfn /mnt/galaxy/tools/hyphy/default /mnt/galaxy/galaxy-app/tool-data/HYPHYI am using a fasta alignment file of 6 protein sequences (566 AA each) as a test case (*also fails with nucleotide alignments).It runs briefly and then issues an error statement "Single Alignment Analyses Segmentation fault (core dumped)".Thank you in advance,
Karen--Karen H. Miga, PhD
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ--Karen H. Miga, PhD--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ