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?

Karen

On 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!

Karen

On 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/HYPHY

I 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

Postdoctoral Scholar
University of California, Santa Cruz
(831)459-5232