Re: [galaxy-dev] Galaxy: Dependency error htseq_count
Glad that everything works now for you. The Get Updates functionality won't work since this is a new version of the tool (updated version of HTSeq package). Since the updated version could generate different results with the same input, Galaxy keeps the old version around for reproducibility reasons. I don't know why you have to restart Galaxy for the tool to show up. As far as I know, that should not be necessary, and also shouldn't be dependent on anything in the tool wrapper configuration. I'm aware of the issue with the screenshot missing. I'm not sure how to get the tool wrapper to point to the static images installed from the toolshed (or if that's even possible). In the meantime, a workaround would be to copy the count_modes.png file from the repository to the [GALAXY_HOME]/static/images directory. Lance Joachim Jacob | VIB | wrote: *sorry for my late reply - we have experienced some email issues lately * Thanks, a clean install from the new versions works! Unfortunately, the 'get updates' from the admin interface of Galaxy does not find any updates with the old version. So, I searched the main toolshed, and I was able to install the new version next to the old (instead of updating). The install succeeded, but I always have to restart Galaxy to get the tool available in the toolbox. One small remark: the screenshot in the tool's interface below the parameters is not shown. Cheers Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 03/11/2013 06:34 PM, Lance Parsons wrote: I have posted an updated version of the htseq-count tool in the toolshed that uses and updated version of the HTSEQ count package (0.5.4p1) and hopefully addresses the installation issue you have experienced. Please try it out and let me know if you still have problems. Lance Joachim Jacob | VIB | wrote: Hi Lance, [apologies for directly emailing to you and not through the galaxy-dev list. I will post it on the dev list later on] I am trying to install htseq-count, but it fails during the dependency installation of htseq. The error I get is: error: can't create or remove files in install directory The following error occurred while trying to add or remove files in the installation directory: [Errno 2] No such file or directory: '/apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/test-easy-install-30482.pth' The installation directory you specified (via --install-dir, --prefix, or the distutils default setting) was: /apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/ This directory does not currently exist. Please create it and try again, or choose a different installation directory (using the -d or --install-dir option). Any idea whether it is related to my setup (and what I can do about it)? Note: only the htseq_count dependency is not being installed. Thanks for providing the htseq_count wrapper! Now getting it through the toolshed will make it again a little closer to a perfect world :-) Cheers, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 12/17/2012 05:28 PM, Lance Parsons wrote: Thanks for looking into this Greg. The environment where I'm having this problem is our testing and production systems. Both environments are CentOS release 5.8 (Final) with Mercurial version 2.4.1. Interestingly, when I tried the same thing with a development setup on my OSX box (10.6.8) with Mercurial 2.4 I did not have the same issue. One difference is that on my testing/production boxes I do have an older version of the tool installed, so perhaps that is the issue. I also tried uninstalling, but that led to the (expected) error that that a previous changeset is installed: The tool shed repository htseq_count with owner lparsons and changeset revision f320093f1e8e was previously installed using changeset revision 5d969cb56112. The repository has been uninstalled, however, so reinstall the original repository instead of installing it again. You can get the latest updates for the repository using the Get updates option from the repository's Repository Actions pop-up menu. Click here to manage the repository. I then attempted to reinstall and I got a javascript message the cloning failed, and the repo is now stuck in the cloning state. I did not see anything in the paster logs regarding this at all. Here are the steps I took on my local system: 1. Upload htseq-count v0.3 to local toolshed 2. Install on local galaxy 3. Upload htseq-count v0.3-release2 to toolshed [Errno 2] No such file or directory: '/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/database/community_files/000/repo_3/./tool_data_table_conf.xml.sample' STDOUT from paster
Re: [galaxy-dev] Galaxy: Dependency error htseq_count
I have posted an updated version of the htseq-count tool in the toolshed that uses and updated version of the HTSEQ count package (0.5.4p1) and hopefully addresses the installation issue you have experienced. Please try it out and let me know if you still have problems. Lance Joachim Jacob | VIB | wrote: Hi Lance, [apologies for directly emailing to you and not through the galaxy-dev list. I will post it on the dev list later on] I am trying to install htseq-count, but it fails during the dependency installation of htseq. The error I get is: error: can't create or remove files in install directory The following error occurred while trying to add or remove files in the installation directory: [Errno 2] No such file or directory: '/apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/test-easy-install-30482.pth' The installation directory you specified (via --install-dir, --prefix, or the distutils default setting) was: /apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/ This directory does not currently exist. Please create it and try again, or choose a different installation directory (using the -d or --install-dir option). Any idea whether it is related to my setup (and what I can do about it)? Note: only the htseq_count dependency is not being installed. Thanks for providing the htseq_count wrapper! Now getting it through the toolshed will make it again a little closer to a perfect world :-) Cheers, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 12/17/2012 05:28 PM, Lance Parsons wrote: Thanks for looking into this Greg. The environment where I'm having this problem is our testing and production systems. Both environments are CentOS release 5.8 (Final) with Mercurial version 2.4.1. Interestingly, when I tried the same thing with a development setup on my OSX box (10.6.8) with Mercurial 2.4 I did not have the same issue. One difference is that on my testing/production boxes I do have an older version of the tool installed, so perhaps that is the issue. I also tried uninstalling, but that led to the (expected) error that that a previous changeset is installed: The tool shed repository htseq_count with owner lparsons and changeset revision f320093f1e8e was previously installed using changeset revision 5d969cb56112. The repository has been uninstalled, however, so reinstall the original repository instead of installing it again. You can get the latest updates for the repository using the Get updates option from the repository's Repository Actions pop-up menu. Click here to manage the repository. I then attempted to reinstall and I got a javascript message the cloning failed, and the repo is now stuck in the cloning state. I did not see anything in the paster logs regarding this at all. Here are the steps I took on my local system: 1. Upload htseq-count v0.3 to local toolshed 2. Install on local galaxy 3. Upload htseq-count v0.3-release2 to toolshed [Errno 2] No such file or directory: '/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/database/community_files/000/repo_3/./tool_data_table_conf.xml.sample' STDOUT from paster htseq-count.xml does not exist! sam_fa_indices.loc.sample does not exist! static/images/count_modes.png does not exist! test-data/htseq-test-paired.bam does not exist! test-data/htseq-test-paired_counts.tsv does not exist! test-data/htseq-test-paired_othercounts.tsv does not exist! test-data/htseq-test.bam does not exist! test-data/htseq-test.gff does not exist! test-data/htseq-test.sam does not exist! test-data/htseq-test_counts.tsv does not exist! test-data/htseq-test_othercounts.tsv does not exist! tool_data_table_conf.xml.sample does not exist! 4. Second attempt to upload The file 'htseq-count_0.3.release2.tar.gz' has been successfully uncompressed and uploaded to the repository. 1 undesirable items (.hg .svn .git directories, .DS_Store, hgrc files, etc) were removed from the archive. 13 files were removed from the repository root. 5. Get repository updates The installed repository named 'htseq_count' has been updated to change set revision '74a6a8221337'. Greg Von Kuster wrote: Hi Lance, I tried several scenarios today in an attempt to reproduce this but I was not able to. Have you tried uninstalling the repository (check the checkbox to completely uninstall it) and then reinstall it? I'm trying to reproduce this on a mac running mercurial version 2.2.3 and Python 2.5. What's your environment? Greg Von Kuster On Dec 13, 2012, at 2:30 PM, Lance Parsons wrote: Since I've had issues with workflow and the toolshed in the past, I have changed my workflow so that my only interaction with the toolshed is either via uploading a tarball via the web interface or installing a tool into my local Galaxy via the web
[galaxy-dev] Galaxy: Dependency error htseq_count
Hi Lance, [apologies for directly emailing to you and not through the galaxy-dev list. I will post it on the dev list later on] I am trying to install htseq-count, but it fails during the dependency installation of htseq. The error I get is: error: can't create or remove files in install directory The following error occurred while trying to add or remove files in the installation directory: [Errno 2] No such file or directory: '/apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/test-easy-install-30482.pth' The installation directory you specified (via --install-dir, --prefix, or the distutils default setting) was: /apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/ This directory does not currently exist. Please create it and try again, or choose a different installation directory (using the -d or --install-dir option). Any idea whether it is related to my setup (and what I can do about it)? Note: only the htseq_count dependency is not being installed. Thanks for providing the htseq_count wrapper! Now getting it through the toolshed will make it again a little closer to a perfect world :-) Cheers, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 12/17/2012 05:28 PM, Lance Parsons wrote: Thanks for looking into this Greg. The environment where I'm having this problem is our testing and production systems. Both environments are CentOS release 5.8 (Final) with Mercurial version 2.4.1. Interestingly, when I tried the same thing with a development setup on my OSX box (10.6.8) with Mercurial 2.4 I did not have the same issue. One difference is that on my testing/production boxes I do have an older version of the tool installed, so perhaps that is the issue. I also tried uninstalling, but that led to the (expected) error that that a previous changeset is installed: The tool shed repository htseq_count with owner lparsons and changeset revision f320093f1e8e was previously installed using changeset revision 5d969cb56112. The repository has been uninstalled, however, so reinstall the original repository instead of installing it again. You can get the latest updates for the repository using the Get updates option from the repository's Repository Actions pop-up menu. Click here to manage the repository. I then attempted to reinstall and I got a javascript message the cloning failed, and the repo is now stuck in the cloning state. I did not see anything in the paster logs regarding this at all. Here are the steps I took on my local system: 1. Upload htseq-count v0.3 to local toolshed 2. Install on local galaxy 3. Upload htseq-count v0.3-release2 to toolshed [Errno 2] No such file or directory: '/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/database/community_files/000/repo_3/./tool_data_table_conf.xml.sample' STDOUT from paster htseq-count.xml does not exist! sam_fa_indices.loc.sample does not exist! static/images/count_modes.png does not exist! test-data/htseq-test-paired.bam does not exist! test-data/htseq-test-paired_counts.tsv does not exist! test-data/htseq-test-paired_othercounts.tsv does not exist! test-data/htseq-test.bam does not exist! test-data/htseq-test.gff does not exist! test-data/htseq-test.sam does not exist! test-data/htseq-test_counts.tsv does not exist! test-data/htseq-test_othercounts.tsv does not exist! tool_data_table_conf.xml.sample does not exist! 4. Second attempt to upload The file 'htseq-count_0.3.release2.tar.gz' has been successfully uncompressed and uploaded to the repository. 1 undesirable items (.hg .svn .git directories, .DS_Store, hgrc files, etc) were removed from the archive. 13 files were removed from the repository root. 5. Get repository updates The installed repository named 'htseq_count' has been updated to change set revision '74a6a8221337'. Greg Von Kuster wrote: Hi Lance, I tried several scenarios today in an attempt to reproduce this but I was not able to. Have you tried uninstalling the repository (check the checkbox to completely uninstall it) and then reinstall it? I'm trying to reproduce this on a mac running mercurial version 2.2.3 and Python 2.5. What's your environment? Greg Von Kuster On Dec 13, 2012, at 2:30 PM, Lance Parsons wrote: Since I've had issues with workflow and the toolshed in the past, I have changed my workflow so that my only interaction with the toolshed is either via uploading a tarball via the web interface or installing a tool into my local Galaxy via the web interface (or occasionally just downloading tarballs). In this specific case, I uploaded a tar.gz file of the entire tool wrapper directory. I did NOT increment the tool version. In the past, incrementing the tool version has generally worked fine. However, when I leave the tool version the same, but change
Re: [galaxy-dev] Galaxy: Dependency error htseq_count
Hi Joachim, It seems that the error is because your system is trying to install the library files to lib64/python instead of just lib/python. For reasons I don't quite understand, the setup.py installation fails when that directory doesn't exist (I would think it would just create it, but that doesn't appear to be the case). As a quick fix, you might try creating the directory /apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/. Create it as the user that galaxy runs under so make sure galaxy has permissions later. Then try reinstalling the dependency. I'm not sure that will work, but that is the gist of the problem. I noticed there is an update to the htseq-count package, so I'll try to put out a new version of the wrapper with a fix for that as well as the new version. Let me know if you still have trouble or if you find some sort of workaround or fix. I'd like to make the installation more robust. Lance Joachim Jacob | VIB | wrote: Hi Lance, [apologies for directly emailing to you and not through the galaxy-dev list. I will post it on the dev list later on] I am trying to install htseq-count, but it fails during the dependency installation of htseq. The error I get is: error: can't create or remove files in install directory The following error occurred while trying to add or remove files in the installation directory: [Errno 2] No such file or directory: '/apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/test-easy-install-30482.pth' The installation directory you specified (via --install-dir, --prefix, or the distutils default setting) was: /apps/htseq/0.5.3p9/lparsons/htseq_count/f320093f1e8e/lib64/python/ This directory does not currently exist. Please create it and try again, or choose a different installation directory (using the -d or --install-dir option). Any idea whether it is related to my setup (and what I can do about it)? Note: only the htseq_count dependency is not being installed. Thanks for providing the htseq_count wrapper! Now getting it through the toolshed will make it again a little closer to a perfect world :-) Cheers, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 12/17/2012 05:28 PM, Lance Parsons wrote: Thanks for looking into this Greg. The environment where I'm having this problem is our testing and production systems. Both environments are CentOS release 5.8 (Final) with Mercurial version 2.4.1. Interestingly, when I tried the same thing with a development setup on my OSX box (10.6.8) with Mercurial 2.4 I did not have the same issue. One difference is that on my testing/production boxes I do have an older version of the tool installed, so perhaps that is the issue. I also tried uninstalling, but that led to the (expected) error that that a previous changeset is installed: The tool shed repository htseq_count with owner lparsons and changeset revision f320093f1e8e was previously installed using changeset revision 5d969cb56112. The repository has been uninstalled, however, so reinstall the original repository instead of installing it again. You can get the latest updates for the repository using the Get updates option from the repository's Repository Actions pop-up menu. Click here to manage the repository. I then attempted to reinstall and I got a javascript message the cloning failed, and the repo is now stuck in the cloning state. I did not see anything in the paster logs regarding this at all. Here are the steps I took on my local system: 1. Upload htseq-count v0.3 to local toolshed 2. Install on local galaxy 3. Upload htseq-count v0.3-release2 to toolshed [Errno 2] No such file or directory: '/Users/lparsons/Documents/projects/sequencing/galaxy/galaxy-test1/database/community_files/000/repo_3/./tool_data_table_conf.xml.sample' STDOUT from paster htseq-count.xml does not exist! sam_fa_indices.loc.sample does not exist! static/images/count_modes.png does not exist! test-data/htseq-test-paired.bam does not exist! test-data/htseq-test-paired_counts.tsv does not exist! test-data/htseq-test-paired_othercounts.tsv does not exist! test-data/htseq-test.bam does not exist! test-data/htseq-test.gff does not exist! test-data/htseq-test.sam does not exist! test-data/htseq-test_counts.tsv does not exist! test-data/htseq-test_othercounts.tsv does not exist! tool_data_table_conf.xml.sample does not exist! 4. Second attempt to upload The file 'htseq-count_0.3.release2.tar.gz' has been successfully uncompressed and uploaded to the repository. 1 undesirable items (.hg .svn .git directories, .DS_Store, hgrc files, etc) were removed from the archive. 13 files were removed from the repository root. 5. Get repository updates The installed repository named 'htseq_count' has been updated to change set revision '74a6a8221337'.
[galaxy-dev] galaxy dependency
Dear galaxy team thank you a lot for providing a complete solution for biologists to analyse their data, i have one question about galaxy : i see that there are a lot of tools for example for ngs, and i could not understand or find the tool in galaxy directories, is that means that all the tool are rewritten in python ? eg bowtie, samtools, fastx and ... Or the binaries are located in some folder that i can not see . thanks ___ 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/
Re: [galaxy-dev] galaxy dependency
Hello, These types of tools are not rewritten, but are instead wrapped so that they function within the Galaxy framework. Galaxy, dependent tools, and reference datasets and indexes are all installed separately. For the basic overview, please see: http://getgalaxy.org A list of Tool dependencies is included in this wiki: http://galaxyproject.org/Admin/Tools/Tool Dependencies And all of the administrative details can be found linked from here: http://galaxyproject.org/Admin Hopefully this helps to explain the process, but please let us know if you have more questions, Best, Jen Galaxy team On 2/2/12 7:01 AM, bmou...@jouy.inra.fr wrote: Dear galaxy team thank you a lot for providing a complete solution for biologists to analyse their data, i have one question about galaxy : i see that there are a lot of tools for example for ngs, and i could not understand or find the tool in galaxy directories, is that means that all the tool are rewritten in python ? eg bowtie, samtools, fastx and ... Or the binaries are located in some folder that i can not see . thanks ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
Re: [galaxy-dev] galaxy dependency
If you are using Ubuntu LTS, you can use packages we are developing for Galaxy dependencies on Bio-linux: https://launchpad.net/~nebc/+archive/galaxy This list is currently incomplete, but steadily growing. Perhaps what you need is here already. Best regards, Casey Casey Bergman, Ph.D. Faculty of Life Sciences University of Manchester Michael Smith Building Oxford Road, M13 9PT Manchester, UK Tel: +44-(0)161-275-1713 Lab: +44-(0)161-275-5980 Fax: +44-(0)161-275-5082 skype: caseymbergman Email: casey.berg...@manchester.ac.uk Web: http://bergmanlab.smith.man.ac.uk/ Twitter: http://twitter.com/bergmanlab Begin forwarded message: From: Bicak, Mesude mbi...@ceh.ac.uk Date: 20 December 2011 18:09:50 GMT To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Cc: an...@bx.psu.edu an...@bx.psu.edu, jeremy.goe...@emory.edu jeremy.goe...@emory.edu, cleme...@galaxyproject.org cleme...@galaxyproject.org, Booth, Timothy G. tbo...@ceh.ac.uk, Gweon, Hyun S. hyu...@ceh.ac.uk, fied...@gmail.com fied...@gmail.com, casey.berg...@manchester.ac.uk casey.berg...@manchester.ac.uk Subject: Galaxy Server on Bio-Linux Dear Galaxy Developers, We work in Professor Dawn Field's group (Molecular Evolution and Bioinformatics Research Group) at the NERC Environmental Bioinformatics Centre (NEBC) of the Centre for Ecology and Hydrology (CEH) Research Institute based in Oxford. We develop and distribute Bio-Linux (http://nebc.nerc.ac.uk/tools/bio-linux), which is a customised Ubuntu distribution that comes with 500+ bioinformatics packages. Within our research group we also provide bioinformatics analysis for NERC-funded researchers, and recently started looking into Galaxy as well. It didn't take us long to discover its power and we would like to enable Bio-Linux users to install, run and maintain the Galaxy server with minimal effort, also with the aim to spread the word on Galaxy in Europe! Recently we took on a project with Dr. Casey Bergman from University of Manchester as the Principal Investigator, to package all the necessary Galaxy dependencies for Ubuntu/Bio-Linux. As many pre-requisities are already included with Bio-Linux, we are already some way down this path. New packages that we create will appear in a Launchpad PPA (https://launchpad.net/~nebc/+archive/galaxy). We will be happy to hear any comments regarding these efforts and we hope that this will be a useful resource for all Galaxy users. Once the initial packaging is done, we hope to collaborate with Galaxy team in maintaining and improving this resource. Best wishes, Tim, Soon and Mesude -- Dr. Mesude Bicak mbi...@ceh.ac.uk Bioinformatician Bio-Linux Developer NERC Biomolecular Analysis Facility (NBAF) http://nbaf.nerc.ac.uk NERC Environmental Bioinformatics Centre (NEBC) http://nebc.nerc.ac.uk Molecular Evolution and Bioinformatics Group Centre for Ecology and Hydrology http://ceh.ac.uk Maclean Building, Benson Lane Crowmarsh Gifford Wallingford, Oxfordshire OX10 8BB Office Tel: +44 1491 69 2705-- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. On 2 Feb 2012, at 20:13, Jennifer Jackson wrote: Hello, These types of tools are not rewritten, but are instead wrapped so that they function within the Galaxy framework. Galaxy, dependent tools, and reference datasets and indexes are all installed separately. For the basic overview, please see: http://getgalaxy.org A list of Tool dependencies is included in this wiki: http://galaxyproject.org/Admin/Tools/Tool Dependencies And all of the administrative details can be found linked from here: http://galaxyproject.org/Admin Hopefully this helps to explain the process, but please let us know if you have more questions, Best, Jen Galaxy team On 2/2/12 7:01 AM, bmou...@jouy.inra.fr wrote: Dear galaxy team thank you a lot for providing a complete solution for biologists to analyse their data, i have one question about galaxy : i see that there are a lot of tools for example for ngs, and i could not understand or find the tool in galaxy directories, is that means that all the tool are rewritten in python ? eg bowtie, samtools, fastx and ... Or the binaries are located in some folder that i can not see . thanks ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support
