Re: [galaxy-dev] Including descriptions etc in extended BLAST+ tabular output
Hi, On Fri, Nov 29, 2013 at 3:26 PM, Jim Johnson johns...@umn.edu wrote: Peter, It's good news that the description field is available in tabular format. That has been the primary reason for using the xml format. Yes. The tabular format allows use of the task parallel feature. We already support parallel sub-tasks with BLAST XML merge support - but yes this is simpler with tabular output. I think you have good default options for output format. Great. I'll probably merge the c25 branch and push that to the Test Tool Shed next week (adding the descriptions as a new 25th column to the default extended tabular output). +1 The 24 column output will be replaced, right? But, I would think we should offer the option to get all available result information. The multi-select checkboxes could serve that purpose. OK, so adding a pick-you-own columns tabular output would be useful :) +1 Cheers, Bjoern Is NCBI good about maintaining the column position of their tabular over successive versions? When picking the columns, the order is the order given at the command line itself - i.e. we would control that in the wrapper explicitly. Regards, Peter ___ 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/
Re: [galaxy-dev] Error running Clustalw and HyPhy on Cloudman
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 khm...@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.laza...@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 ___ 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/
Re: [galaxy-dev] Error running Clustalw and HyPhy on Cloudman
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.laza...@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 khm...@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.laza...@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 ___ 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/
Re: [galaxy-dev] Error running Clustalw and HyPhy on Cloudman
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 khm...@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? Karen On Sun, Dec 1, 2013 at 2:00 PM, Ross ross.laza...@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 khm...@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.laza...@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 -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J ___ 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/
Re: [galaxy-dev] Error running Clustalw and HyPhy on Cloudman
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.laza...@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 khm...@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? Karen On Sun, Dec 1, 2013 at 2:00 PM, Ross ross.laza...@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 khm...@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.laza...@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 -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J -- Karen H. Miga, PhD Postdoctoral Scholar University of California, Santa Cruz (831)459-5232 ___ 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/
Re: [galaxy-dev] Error running Clustalw and HyPhy on Cloudman
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 khm...@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. Karen On Sun, Dec 1, 2013 at 2:10 PM, Ross ross.laza...@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 khm...@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? Karen On Sun, Dec 1, 2013 at 2:00 PM, Ross ross.laza...@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 khm...@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.laza...@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 -- Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=enuser=UCUuEM4J -- 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=enuser=UCUuEM4J ___ 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:
Re: [galaxy-dev] Error running Clustalw and HyPhy on Cloudman
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.laza...@gmail.com 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 khm...@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. Karen On Sun, Dec 1, 2013 at 2:10 PM, Ross ross.laza...@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 khm...@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? Karen On Sun, Dec 1, 2013 at 2:00 PM, Ross ross.laza...@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 khm...@soe.ucsc.eduwrote: 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.laza...@gmail.comwrote: 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=enuser=UCUuEM4J -- 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
Re: [galaxy-dev] Error running Clustalw and HyPhy on Cloudman
ah. you are right - I had not updated that older repository - I think I was waiting for confirmation that the testtoolshed version worked - will do shortly - thanks for pointing that out! Try removing that one completely and then installing the test toolshed version please? That should work until I get the main one updated in a few hours. On Mon, Dec 2, 2013 at 9:28 AM, Karen Miga khm...@soe.ucsc.edu wrote: 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.laza...@gmail.com 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 khm...@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. Karen On Sun, Dec 1, 2013 at 2:10 PM, Ross ross.laza...@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 khm...@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? Karen On Sun, Dec 1, 2013 at 2:00 PM, Ross ross.laza...@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 khm...@soe.ucsc.eduwrote: 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.laza...@gmail.comwrote: 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
Re: [galaxy-dev] hmmer install
Hello Karen, You are undoubtedly seeing only the hmmpress tool because the other tool in that repository is not valid: Contents of this repository Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata NameDescription Version hmmpressCompress profile db 1.0.0 Invalid tools - click the tool config file name to see why the tool is invalid hmmer.xml If you click on the invalid tool in the tool shed, you'll see the reason that it is invalid: hmmer.xml - This file refers to a file named hmmdb.loc. Upload a file named hmmdb.loc.sample to the repository to correct this error. You should also see an exception thrown in your paster when you start your Galaxy instance telling you why the tool is not being loaded into Galaxy. It look like this repository is missing a file named hmmdb.loc.sample that should provide sample entries for the Galaxy data tables that this tool must use. I'm not sure of the layout of this table for this particular tool, but if you discover what it should be, you can manually add them into a file named hmmdb.loc in the ~/tool-data directory in your Galaxy environment. Greg Von Kuster On Dec 1, 2013, at 4:44 PM, Karen Miga khm...@soe.ucsc.edu wrote: Hello, I would like to use hmmer on our cloudman instance. However, when I install I am only finding a wrapper for hmmpress. There was some conversation about this back in 2012 (http://gmod.827538.n3.nabble.com/Missing-tool-previews-in-tool-shed-e-g-hmmer-xml-td3838635.html). I installed the hmmer package 3.0 and 3.1 from the toolshed as well, however, I am not seeing a wrapper for these tools - perhaps I am missing something? Best wishes, 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/
Re: [galaxy-dev] hmmer install
Hi Greg, Thanks for the feedback. I cannot seem to find information for hmmdb.loc. When I look in the associated xml file it looks like it could be removed completely (does one need a precompiled HMM Database? I do not remember using anything like this when I run hmmer on the commandline). I have less experience with changing wrappers, etc. Have you tried just commenting this part out? And do I need to start the instance over to test it? Thanks in advance! - Karen conditional name=hmmdb param name=select type=select label=HMM Db option value=db selected=TruePrecompiled HMM Database/option option value=userHMM Database in your History/option /param when value=db param name=file type=select label=Precompiled HMM database options from_file=hmmdb.loc column name=name index=1/ column name=value index=2/ /options /param /when when value=user param name=file type=data format=hmmer label=HMM database / /when /conditional On Sun, Dec 1, 2013 at 5:32 PM, Greg Von Kuster g...@bx.psu.edu wrote: Hello Karen, You are undoubtedly seeing only the hmmpress tool because the other tool in that repository is not valid: Contents of this repository Valid tools* - click the name to preview the tool and use the pop-up menu to inspect all metadata*http://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=nameoperation=view_or_manage_repositoryid=e7e502574a48abf0async=falseshow_item_checkboxes=falsef-free-text-search=hmmerpage=1 NameDescriptionVersion hmmpresshttp://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=e7e502574a48abf0render_repository_actions_for=tool_shedtool_config=database%2Fcommunity_files%2F000%2Frepo_148%2Fhmmpress.xmlchangeset_revision=c0fb858f44a2 Compress profile db1.0.0 Invalid tools* - click the tool config file name to see why the tool is invalid*http://toolshed.g2.bx.psu.edu/repository/manage_repository?sort=nameoperation=view_or_manage_repositoryid=e7e502574a48abf0async=falseshow_item_checkboxes=falsef-free-text-search=hmmerpage=1 hmmer.xmlhttp://toolshed.g2.bx.psu.edu/repository/load_invalid_tool?repository_id=e7e502574a48abf0render_repository_actions_for=tool_shedtool_config=hmmer.xmlchangeset_revision=c0fb858f44a2 If you click on the invalid tool in the tool shed, you'll see the reason that it is invalid: *hmmer.xml* - This file refers to a file named *hmmdb.loc*. Upload a file named *hmmdb.loc.sample* to the repository to correct this error. You should also see an exception thrown in your paster when you start your Galaxy instance telling you why the tool is not being loaded into Galaxy. It look like this repository is missing a file named hmmdb.loc.sample that should provide sample entries for the Galaxy data tables that this tool must use. I'm not sure of the layout of this table for this particular tool, but if you discover what it should be, you can manually add them into a file named hmmdb.loc in the ~/tool-data directory in your Galaxy environment. Greg Von Kuster On Dec 1, 2013, at 4:44 PM, Karen Miga khm...@soe.ucsc.edu wrote: Hello, I would like to use hmmer on our cloudman instance. However, when I install I am only finding a wrapper for hmmpress. There was some conversation about this back in 2012 ( http://gmod.827538.n3.nabble.com/Missing-tool-previews-in-tool-shed-e-g-hmmer-xml-td3838635.html). I installed the hmmer package 3.0 and 3.1 from the toolshed as well, however, I am not seeing a wrapper for these tools - perhaps I am missing something? Best wishes, 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/ -- Karen H. Miga, PhD Postdoctoral Scholar University of California, Santa Cruz (831)459-5232 ___ 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/
[galaxy-dev] December 2013 Galaxy Update
Hello all, The final *Galaxy Update* newsletter of 2013http://wiki.galaxyproject.org/GalaxyUpdates/2013_12 is out: - Three new public Galaxy servershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#A50.2B-_Public_Servers , *bringing the total to over 50.* - 61 new papershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#New_Papers (a new monthly record) - Who's hiringhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#Who.27s_Hiring at seven different institutions - Upcoming Eventshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#Events, including - Save these dates! GCC2014: June 30 - July 2, Baltimorehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#GCC2014:_June_30_-_July_2.2C_Baltimore - Sponsorshipshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#Sponsorships and Exhibitorshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#Exhibitors - UC Davis Bioinformatics Boot Campshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#UC_Davis_Bioinformatics_Boot_Camps - Distributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#Galaxy_Distributions - Tool Shed contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#ToolShed_Contributions (including a new ToolShedhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#New_Public_ToolSheds ) - Other Newshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_12#Other_News If you have anything you would like to see in the next *Galaxy Update http://wiki.galaxyproject.org/GalaxyUpdates*, please let us know. Thanks for an excellent year, Dave Clements and the Galaxy Team http://wiki.galaxyproject.org/GalaxyTeam -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/
