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 htseq-c
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 in
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'. G
