Re: [galaxy-dev] Reference Genome in snpEff Tool
Hi Xiaofei, It is best to keep replied on the mailing list. First, confirm that you are running the most current version of the Galaxy distribution. This should be true by default if the installation was just performed. https://wiki.galaxyproject.org/DevNewsBriefs https://wiki.galaxyproject.org/DevNewsBriefs/2014_02_10 Since you ran into this issue the first time the server was brought up (or this appears to be the case), you may have run into a characterized issue. On the http://getgalaxy.org page, are two work-arounds for installing eggs in under specific usage circumstances. One is for when running without internet access (probably not the issue). The other is for when using Python 2.7 (my best guess as the problem). Both are included about half-way down the wiki page, toward the end of the 'Start it up' section: https://wiki.galaxyproject.org/Admin/GetGalaxy Please review and see if either if these apply, in particular if the second command (sh run.sh --reload) solves the issue. Again, please keep feedback on the list, so that the developers can assist us going forward as needed, Jen Galaxy team On 2/24/14 9:51 AM, Wang, Xiaofei wrote: Dear Jen, I really appreciate for your reply! We decided to install the local Galaxy for this project. But, when I installed it (I followed the instruction on these 2 links, http://gmod.org/wiki/Galaxy_Tutorial_2013 and https://wiki.galaxyproject.org/Admin/GetGalaxy), I got a problem like this: $ sh run.sh Some eggs are out of date, attempting to fetch... Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 37, in module c.resolve() # Only fetch eggs required by the config File /Volumes/saturn/xiaofei/software/galaxy-dist/lib/galaxy/eggs/__init__.py, line 345, in resolve egg.resolve() File /Volumes/saturn/xiaofei/software/galaxy-dist/lib/galaxy/eggs/__init__.py, line 195, in resolve return self.version_conflict( e.args[0], e.args[1] ) File /Volumes/saturn/xiaofei/software/galaxy-dist/lib/galaxy/eggs/__init__.py, line 226, in version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg.fetch ) File /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/pkg_resources.py, line 576, in resolve raise DistributionNotFound(req) pkg_resources.DistributionNotFound: pysam==0.4.2-kanwei-b10f6e722e9a Fetch failed. It seems a problem with the Python 'eggs. But, when I checked the version of Python, it is: $ python --version Python 2.7.6 Could you help me about what is the problem with the installation? Thank you so much! Best, Xiaofei ___ 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] Reference Genome in snpEff Tool
Howdy! I only see the Caenorhabditis elegans: WS220.64 reference genome listed in the Genome drop down menu in the snpEff tool. If possible, I would like to use the latest human genome hg19. Can it be added as an option? Thanks in advance. Not: I did follow the link to the developer's site, but would prefer to use the tool from within Galaxy. Clint Christensen Research Assistant, Department of Genetics Texas Biomedical Research Institute 7620 NW Loop 410 San Antonio, TX 78245 210-258-9779 cli...@txbiomedgenetics.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/
Re: [galaxy-dev] Reference Genome in snpEff Tool
I have the same question. But, I want to use it on Drosophila and use SnpEff for CloudMap pipeline. From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Clint Christensen [cli...@txbiomedgenetics.org] Sent: Monday, February 17, 2014 10:01 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Reference Genome in snpEff Tool Howdy! I only see the Caenorhabditis elegans: WS220.64 reference genome listed in the Genome drop down menu in the snpEff tool. If possible, I would like to use the latest human genome hg19. Can it be added as an option? Thanks in advance. Not: I did follow the link to the developer's site, but would prefer to use the tool from within Galaxy. Clint Christensen Research Assistant, Department of Genetics Texas Biomedical Research Institute 7620 NW Loop 410 San Antonio, TX 78245 210-258-9779 cli...@txbiomedgenetics.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/ ___ 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] Reference Genome in snpEff Tool
Hi Clint, Xiaofei, There are no current plans to include additional genomes to the SnpEff tool on the public Main Galaxy instance at http://usegalaxy.org. The best solution is to either run a local Galaxy (with sufficient resources) or what is probably easier and more practical for many scientific end users, a cloud Galaxy or possibly a Slipstream Appliance. The tool wrapper is in the Tool Shed, so it can be installed and used within your Galaxy, where you can add in any genome that you want that has the appropriate reference data available. Help to get started is in these links: https://wiki.galaxyproject.org/BigPicture/Choices https://wiki.galaxyproject.org/Tool%20Shed Hopefully one of these solutions will work out for both of you! Jen Galaxy team On 2/17/14 8:20 AM, Wang, Xiaofei wrote: I have the same question. But, I want to use it on Drosophila and use SnpEff for CloudMap pipeline. From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Clint Christensen [cli...@txbiomedgenetics.org] Sent: Monday, February 17, 2014 10:01 AM To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Reference Genome in snpEff Tool Howdy! I only see the Caenorhabditis elegans: WS220.64 reference genome listed in the Genome drop down menu in the snpEff tool. If possible, I would like to use the latest human genome hg19. Can it be added as an option? Thanks in advance. Not: I did follow the link to the developer's site, but would prefer to use the tool from within Galaxy. Clint Christensen Research Assistant, Department of Genetics Texas Biomedical Research Institute 7620 NW Loop 410 San Antonio, TX 78245 210-258-9779 cli...@txbiomedgenetics.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/ ___ 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/ -- Jennifer Hillman-Jackson http://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/
