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(a)gmail.com&gt; 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 > > >

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(a)gmail.com&gt; 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(a)soe.ucsc.edu&gt; 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(a)gmail.com&gt; 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

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. Karen On Sun, Dec 1, 2013 at 2:10 PM, Ross <ross.lazarus(a)gmail.com&gt; 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(a)soe.ucsc.edu&gt; 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? >> >> Karen >> >> >> On Sun, Dec 1, 2013 at 2:00 PM, Ross <ross.lazarus(a)gmail.com&gt; 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(a)soe.ucsc.edu&gt; 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(a)gmail.com&gt; 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 >> > > > > -- > Ross Lazarus MBBS MPH; > Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 > http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ > -- Karen H. Miga, PhD Postdoctoral Scholar University of California, Santa Cruz (831)459-5232

Yes, I do all of my installs from the toolshed through the admin menu, however I did not use the "test toolshed..." I used the main. Ah ha - maybe that was the issue? Karen On Sun, Dec 1, 2013 at 2:23 PM, Ross <ross.lazarus(a)gmail.com&gt; wrote: > 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(a)soe.ucsc.edu&gt; 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. >> >> Karen >> >> >> On Sun, Dec 1, 2013 at 2:10 PM, Ross <ross.lazarus(a)gmail.com&gt; 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(a)soe.ucsc.edu&gt; 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? >>>> >>>> Karen >>>> >>>> >>>> On Sun, Dec 1, 2013 at 2:00 PM, Ross <ross.lazarus(a)gmail.com&gt; 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(a)soe.ucsc.edu&gt;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(a)gmail.com&gt;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 >>>> >>> >>> >>> >>> -- >>> Ross Lazarus MBBS MPH; >>> Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 >>> http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ >>> >> >> >> >> -- >> Karen H. Miga, PhD >> >> Postdoctoral Scholar >> University of California, Santa Cruz >> (831)459-5232 >> > > > > -- > Ross Lazarus MBBS MPH; > Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 > http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ > -- Karen H. Miga, PhD Postdoctoral Scholar University of California, Santa Cruz (831)459-5232