Re: [galaxy-dev] universe_wsgi.ini
Hi Daniel, I have to admit it took me some time and a lot of trial and error to figure out how the .loc files work :) I'm glad it works for you now. I'm not fully sure about what exactly you want to do but here is what I think could be of help: If your Galaxy runs on the same machine your files are stored in, or if the place they are stored is mounted on your Galaxy's machine, don't bother with the upload tool in the analysis panel nor the Shared Data section, use the Admin section Manage data libraries so you can load files from giving Galaxy a filesystem path. This way you can ask it to load the data without moving/copying it. (it's also superfast) Hope that helps, L-A Le 24/02/2012 19:25, Brami, Daniel a écrit : Hi L-A, Thank you for the reply. Another kind member (thanks Dan Dorset!) also took the time to explain me these over the phone this morning. The missing piece of information, which you have included in your instructions, and which was omitted in the documentation, is the link between the bowtie_indices.loc and the builds.txt file, which is never mentioned anywhere as far as I know. As for the file size limit, it's more of a question regarding the understanding of how Galaxy works. In my local copy of Galaxy running on Unix, given an input file using the complete path, does Galaxy need to copy the input data through the browser to the 'tmp' and output directories or does it use a system call. Can this be made into a link to save space and time? I really do appreciate the help -- thanks! Daniel *From:*galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Louise-Amélie Schmitt *Sent:* Friday, February 24, 2012 12:23 AM *To:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy-dev] universe_wsgi.ini Hello Daniel, I had similar issues when setting up our own. The POST size limit is not set by Galaxy. If I remember correctly it's in your Apache config, though I don't remember exactly where it was. For the .loc files, here is an example: dm3-btdm3D.melanogaster 3 /path/to/indexes/bowtie/d_melanogaster_fb5_22 The items are as follows: - dm3-bt is a unique ID for this index. It can be whatever you want but it needs to be unique in this file. - dm3 is the build ID that you set in the tool-data/shared/ucsc/builds.txt file. It's the first item there. It's there to tell what genome build your index was generated from. Make sure that the two of them correspond. - D.melanogaster 3 is the display name that you want to have in the widgets (can have spaces but no tabs) - /path/to/indexes/bowtie/d_melanogaster_fb5_22 is the full path of the index files without the final suffixes (the first part before the first dot) Each line's items must be separated by an actual tab character. Depending on your editor, you might want to make sure the tab key doesn't print like 4 spaces instead of \t. Hope that helps Best, L-A Le 23/02/2012 19:47, Brami, Daniel a écrit : I have been struggling with setting up my local Galaxy instance for the past two days. Can anyone post a copy of their universe_wsgi.ini file , with the sensitive info commented / removed? I need an instance that can handle local files greater than 2 GB (ie: does not go through POST method of browser to get data) and has permissions to use pre-built bowtie indices. Also, a FUNCTIONNAL copy of the 'bowtie_indices.loc' would be very helpful. (none of my prebuilt databases are appearing in drop down menu). Please assist. Daniel Brami Synthetic Genomics, Inc. Senior Research Associate, Bioinformatics 11149 North Torrey Pines Road La Jolla, California 92037 Phone: 858.433.2230 Fax: 858.754.2988 dbr...@syntheticgenomics.com mailto:dbr...@syntheticgenomics.com www.SyntheticGenomics.com http://www.syntheticgenomics.com/ ___ 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/ ___ 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/
[galaxy-dev] can the sample tracking system transfer (copy) data to a dataset library not in private Galaxy server data directory tree and then just link files?
Dear all, Is there a way with the Galaxy sample tracking system to have the dataset transfer feature copy data to a dataset library outside the private Galaxy server data directory tree and then the dataset library just link (like you can do with upload files feature when managing data libraries)? The reason for this is that it is common to have such huge data also available outside of Galaxy on the filesystem for bioinformatians/computational biologists to access directly without having to have two copies. regards, Leandro ___ 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/
[galaxy-dev] Upload file script fails with OSError: [Errno 1]
Hello, I would like to report on a Galaxy issue and the my proposed solution for it, hopefully it will be helpful to other Galaxy users that encounter [are encountering] the same problem. I tried to upload to my local Galaxy a file that I has been transferred by a FTP client. Then, when Galaxy tried to pull out this file from the FTP server, the operation failed with this traceback: File /home/galaxy/galaxy-dist/tools/data_source/upload.py, line 403, in module __main__() File /home/galaxy/galaxy-dist/tools/data_source/upload.py, line 392, in __main__ add_file( dataset, registry, json_file, output_path ) File /home/galaxy/galaxy-dist/tools/data_source/upload.py, line 289, in add_file line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place ) File /home/galaxy/galaxy-dist/lib/galaxy/datatypes/sniff.py, line 98, in convert_newlines shutil.move( temp_name, fname ) File /usr/lib64/python2.6/shutil.py, line 260, in move copy2(src, real_dst) File /usr/lib64/python2.6/shutil.py, line 96, in copy2 copystat(src, dst) File /usr/lib64/python2.6/shutil.py, line 66, in copystat os.utime(dst, (st.st_atime, st.st_mtime)) OSError: [Errno 1] Operation not permitted: '/home/galaxy_upload/data_upload/...' The source file that I tried to copy had read/write permissions for all, therefore, logically, this operation should not have failed... I read a bit about this issue and I found out that python command shutil.move might raise an OSError when it tries to move a file to a partition where the user (galaxy in this case) has write permission but he is not the owner. More specifically, the exception fails to modify the copystat data. I have found a post suggesting to simply IGNORE this OSError that was raised from copystat... Therefore, I added the following try statement to galaxy-dist/lib/galaxy/datatypes/sniff.py on line 98: try: shutil.move( temp_name, fname ) # Return number of lines in file. except OSError: pass return ( i + 1, None ) and it solved the problem completely! This is the link to the post that I took the solution from: http://bugs.python.org/issue1438480 I'm also attaching a modified sniff.py. Hopefully, this will be helpful to other galaxy developers, Best, Liram ___ 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/
[galaxy-dev] Data not uploading in Local instance
Hi Luciano, I am going to forward you question over the to galaxy-...@bx.psu.edu mailing list where the development community will see and provide feedback to your question: http://wiki.g2.bx.psu.edu/Support#Mailing_Lists Best, Jen Galaxy team On 2/26/12 3:19 PM, Luciano Cosme wrote: I have python 2.7 and it seems to be the problem with it. Just formated the partition I had linux and fresh install everything and still have same problem. I did what is recommended here too. Check your Python version Galaxy's core functionality is compatible with *Python* versions *2.5*, *2.6*, and *2.7*. (Version 2.4 support was last included in the November 18, 2011 Distribution http://wiki.g2.bx.psu.edu/DevNewsBriefs/2011_11_18#Python_Support). Before reporting bugs, please ensure that python --version reports one of these three versions. If this is not the case, a simple solution is to manipulate your shell's $PATH variable to place the correct version first. This can be done for only Python by creating a new directory at the front of $PATH and creating a symbolic link to python in that directory: Toggle line numbers http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy# 1 http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy#CA-78df7933c2e9e4b1411a7e60fd3087c684c79664_1 % mkdir ~/galaxy-python 2 http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy#CA-78df7933c2e9e4b1411a7e60fd3087c684c79664_2 % ln -s /path/to/python2.5 ~/galaxy-python/python 3 http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy#CA-78df7933c2e9e4b1411a7e60fd3087c684c79664_3 %exportPATH=~/galaxy-python:$PATH On Sat, Feb 25, 2012 at 5:50 PM, Luciano Cosme cosme.sim...@gmail.com mailto:cosme.sim...@gmail.com wrote: *Hi Everyone, I have been running a Local Galaxy instance for a long time, but now I am having some problems with uploading data. I am getting the following error:* Can't create peek [Errno 2] No such file or directory:'/home/koala2/galaxy-dist/database/files/000/dataset_13.dat' * and from the Terminal:* 127.0.0.1 - - [25/Feb/2012:17:45:00 -0500]POST /library_common/library_item_updates HTTP/1.1 200 -http://127.0.0.1:8080/library_common/browse_library? sort=nameoperation=browsef-description=Allf-name=Allf-deleted=Falsecntrller=library_adminasync=falseshow_item_checkboxes=falsewebapp= galaxyid=f2db41e1fa331b3epage=1 Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2 *I reinstalled Unbutu and still having the same issue. I also removed Postgresql 9.1 and reinstalled it. I that it might be an issue with postgresql and not Galaxy, but I am not an expert. Any suggestions will be appreciated. Thank you. Luciano * ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/
[galaxy-dev] Trouble linking to/displaying at local Genome Browser
Hello all, I am having some trouble getting a display at link to my local UCSC Genome Browser mirror to show up under my Galaxy jobs for viewing, although I can get the link to the online UCSC GB to display. I followed the suggestions in the following thread but it has yielded no results yet: http://gmod.827538.n3.nabble.com/using-local-Genome-Browser-mirror-td1829290.html . Here's what I have tried: - I edited the [galaxy-dir]/tool-data/shared/ucsc/ucsc_build_sites.txt file and duplicated the 'main' UCSC entry but changed the new entry's name to 'internalgb' and changed the URL to point to our local GB with * cgi-bin/hgTracks?* at the end - I set *ucsc_display_sites = internalgb* in universe_wsgi.ini - I made a modified copy of [galaxy-dir]/tools/data_source/ucsc_tablebrowser.xml (named HAIB_ucsc_tablebrowser.xml) in the same directory as the other XML files and created a tool link on the left side of the Galaxy page for it by adding it to the tool_conf.xml file (which works fine: when I click on it it loads our local Genome Browser inside the central Galaxy window frame) - I edited the HAIB_ucsc_tablebrowser.xml file according to the recommendation in the thread above: *I had to change the name and id of the tool in the new ucsc_tablebrowser.xml file, and keep the id the same for the param.toold_id.value as well*. So I gave it a unique id (changed ucsc_table_direct1 to HAIB_table_direct1) but kept the tool_id value field the same as the original/main UCSC tablebrowser (ucsc_table_direct1). Then I put the new HAIB id for our local tablebrowser into universe_wsgi.ini under the tool runners section as *HAIB_table_direct1 = local:///* - And of course I have restarted Galaxy after each change. Still after all of this I cannot see a display at link for bam other files from Galaxy for my local UCSC GB. When I change universe_wsgi.ini to have ucsc_display_sites = internalgb,main set (for both browsers) the online/main GB will have a display at link on Galaxy jobs but no link shows for my local browser mirror. I'm also a little fuzzy on the relation between the ucsc_build_sites.txt file and the *_ucsc_tablebrowser.xml files (if any). Any tips as to what I might be missing here? Thanks! Josh ___ 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] Trouble linking to/displaying at local Genome Browser
Hi Josh, It sounds like you are really close to getting this to work. My first guess would be that there is an issue with the modified ucsc_build_sites.txt file. Can you check that the line you copied is tab delimited and not space delimited? Thanks for using Galaxy, Dan On Feb 27, 2012, at 11:46 AM, Josh Nielsen wrote: Hello all, I am having some trouble getting a display at link to my local UCSC Genome Browser mirror to show up under my Galaxy jobs for viewing, although I can get the link to the online UCSC GB to display. I followed the suggestions in the following thread but it has yielded no results yet: http://gmod.827538.n3.nabble.com/using-local-Genome-Browser-mirror-td1829290.html. Here's what I have tried: - I edited the [galaxy-dir]/tool-data/shared/ucsc/ucsc_build_sites.txt file and duplicated the 'main' UCSC entry but changed the new entry's name to 'internalgb' and changed the URL to point to our local GB with cgi-bin/hgTracks? at the end - I set ucsc_display_sites = internalgb in universe_wsgi.ini - I made a modified copy of [galaxy-dir]/tools/data_source/ucsc_tablebrowser.xml (named HAIB_ucsc_tablebrowser.xml) in the same directory as the other XML files and created a tool link on the left side of the Galaxy page for it by adding it to the tool_conf.xml file (which works fine: when I click on it it loads our local Genome Browser inside the central Galaxy window frame) - I edited the HAIB_ucsc_tablebrowser.xml file according to the recommendation in the thread above: I had to change the name and id of the tool in the new ucsc_tablebrowser.xml file, and keep the id the same for the param.toold_id.value as well. So I gave it a unique id (changed ucsc_table_direct1 to HAIB_table_direct1) but kept the tool_id value field the same as the original/main UCSC tablebrowser (ucsc_table_direct1). Then I put the new HAIB id for our local tablebrowser into universe_wsgi.ini under the tool runners section as HAIB_table_direct1 = local:/// - And of course I have restarted Galaxy after each change. Still after all of this I cannot see a display at link for bam other files from Galaxy for my local UCSC GB. When I change universe_wsgi.ini to have ucsc_display_sites = internalgb,main set (for both browsers) the online/main GB will have a display at link on Galaxy jobs but no link shows for my local browser mirror. I'm also a little fuzzy on the relation between the ucsc_build_sites.txt file and the *_ucsc_tablebrowser.xml files (if any). Any tips as to what I might be missing here? Thanks! Josh ___ 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/ ___ 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] GATK metadata problems
Hi Curt, This is an annoyance when trying to use these tools interactively, but running or designing a workflow in the editor should work just fine. The issue is that for Galaxy the BAM index is technically considered an optional metadata attribute, but it is required for GATK. I've removed the metadata validator from the tool configurations and updated the GATK wrapper script to build missing BAM indexes on the fly as needed in changeset 6745:167fddae9646. Please let us know if you experience further issues. Thanks for using Galaxy, Dan On Feb 24, 2012, at 6:57 PM, Curt Palm wrote: When I try to run a GATK analysis that uses a bam file as input, I get the following error in the html page: Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue. when the input file is a bam file that has not run yet or is still running. So I can not set up multi step analysis or set up a work flow. I searched the mailing lists and could not find info on this, only a thread discussing wanting to use meta data from bam files to set the ref. genomes for GATK tools. is there a solution to this I am using the current version of Galaxy. thanks *** Curtis J. Palm cp...@stanford.edu Stanford Genome Technology Center MC: 8307 office: 650-812-1994cell: 408 858-7849 *** ___ 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/ ___ 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] Trouble linking to/displaying at local Genome Browser
Hi Dan, Good catch sir! Genius! It is working now. The spacing was exactly the same to the eye in vi for all the entries, but once I did a 'set list' in vi to display formatting characters I saw that 'main' had the tab ^I characters but my 'internalgb' entry didn't. This must have happened because I did a visual copy with my cursor. Thank you. -Josh On Mon, Feb 27, 2012 at 11:09 AM, Daniel Blankenberg d...@bx.psu.edu wrote: Hi Josh, It sounds like you are really close to getting this to work. My first guess would be that there is an issue with the modified ucsc_build_sites.txt file. Can you check that the line you copied is tab delimited and not space delimited? Thanks for using Galaxy, Dan On Feb 27, 2012, at 11:46 AM, Josh Nielsen wrote: Hello all, I am having some trouble getting a display at link to my local UCSC Genome Browser mirror to show up under my Galaxy jobs for viewing, although I can get the link to the online UCSC GB to display. I followed the suggestions in the following thread but it has yielded no results yet: http://gmod.827538.n3.nabble.com/using-local-Genome-Browser-mirror-td1829290.html . Here's what I have tried: - I edited the [galaxy-dir]/tool-data/shared/ucsc/ucsc_build_sites.txt file and duplicated the 'main' UCSC entry but changed the new entry's name to 'internalgb' and changed the URL to point to our local GB with * cgi-bin/hgTracks?* at the end - I set *ucsc_display_sites = internalgb* in universe_wsgi.ini - I made a modified copy of [galaxy-dir]/tools/data_source/ucsc_tablebrowser.xml (named HAIB_ucsc_tablebrowser.xml) in the same directory as the other XML files and created a tool link on the left side of the Galaxy page for it by adding it to the tool_conf.xml file (which works fine: when I click on it it loads our local Genome Browser inside the central Galaxy window frame) - I edited the HAIB_ucsc_tablebrowser.xml file according to the recommendation in the thread above: *I had to change the name and id of the tool in the new ucsc_tablebrowser.xml file, and keep the id the same for the param.toold_id.value as well*. So I gave it a unique id (changed ucsc_table_direct1 to HAIB_table_direct1) but kept the tool_id value field the same as the original/main UCSC tablebrowser (ucsc_table_direct1). Then I put the new HAIB id for our local tablebrowser into universe_wsgi.ini under the tool runners section as *HAIB_table_direct1 = local:///* - And of course I have restarted Galaxy after each change. Still after all of this I cannot see a display at link for bam other files from Galaxy for my local UCSC GB. When I change universe_wsgi.ini to have ucsc_display_sites = internalgb,main set (for both browsers) the online/main GB will have a display at link on Galaxy jobs but no link shows for my local browser mirror. I'm also a little fuzzy on the relation between the ucsc_build_sites.txt file and the *_ucsc_tablebrowser.xml files (if any). Any tips as to what I might be missing here? Thanks! Josh ___ 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/ ___ 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] Trouble linking to/displaying at local Genome Browser
One more thing while I'm at it. For clarification would only the first two steps I listed be sufficient to get the display at link in Galaxy? If so what is the benefit of the other steps (other than having an actual link to your local genome browser mirror in Galaxy)? There's nothing that ties my internalgb entry to the new tool_id I created is there? On Mon, Feb 27, 2012 at 11:58 AM, Josh Nielsen jniel...@hudsonalpha.comwrote: Hi Dan, Good catch sir! Genius! It is working now. The spacing was exactly the same to the eye in vi for all the entries, but once I did a 'set list' in vi to display formatting characters I saw that 'main' had the tab ^I characters but my 'internalgb' entry didn't. This must have happened because I did a visual copy with my cursor. Thank you. -Josh On Mon, Feb 27, 2012 at 11:09 AM, Daniel Blankenberg d...@bx.psu.eduwrote: Hi Josh, It sounds like you are really close to getting this to work. My first guess would be that there is an issue with the modified ucsc_build_sites.txt file. Can you check that the line you copied is tab delimited and not space delimited? Thanks for using Galaxy, Dan On Feb 27, 2012, at 11:46 AM, Josh Nielsen wrote: Hello all, I am having some trouble getting a display at link to my local UCSC Genome Browser mirror to show up under my Galaxy jobs for viewing, although I can get the link to the online UCSC GB to display. I followed the suggestions in the following thread but it has yielded no results yet: http://gmod.827538.n3.nabble.com/using-local-Genome-Browser-mirror-td1829290.html . Here's what I have tried: - I edited the [galaxy-dir]/tool-data/shared/ucsc/ucsc_build_sites.txt file and duplicated the 'main' UCSC entry but changed the new entry's name to 'internalgb' and changed the URL to point to our local GB with * cgi-bin/hgTracks?* at the end - I set *ucsc_display_sites = internalgb* in universe_wsgi.ini - I made a modified copy of [galaxy-dir]/tools/data_source/ucsc_tablebrowser.xml (named HAIB_ucsc_tablebrowser.xml) in the same directory as the other XML files and created a tool link on the left side of the Galaxy page for it by adding it to the tool_conf.xml file (which works fine: when I click on it it loads our local Genome Browser inside the central Galaxy window frame) - I edited the HAIB_ucsc_tablebrowser.xml file according to the recommendation in the thread above: *I had to change the name and id of the tool in the new ucsc_tablebrowser.xml file, and keep the id the same for the param.toold_id.value as well*. So I gave it a unique id (changed ucsc_table_direct1 to HAIB_table_direct1) but kept the tool_id value field the same as the original/main UCSC tablebrowser (u csc_table_direct1). Then I put the new HAIB id for our local tablebrowser into universe_wsgi.ini under the tool runners section as *HAIB_table_direct1 = local:///* - And of course I have restarted Galaxy after each change. Still after all of this I cannot see a display at link for bam other files from Galaxy for my local UCSC GB. When I change universe_wsgi.ini to have ucsc_display_sites = internalgb,main set (for both browsers) the online/main GB will have a display at link on Galaxy jobs but no link shows for my local browser mirror. I'm also a little fuzzy on the relation between the ucsc_build_sites.txt file and the *_ucsc_tablebrowser.xml files (if any). Any tips as to what I might be missing here? Thanks! Josh ___ 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/ ___ 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] Trouble linking to/displaying at local Genome Browser
Hi Josh, Correct, to get the display functionality to work, your first two steps are sufficient. The other steps are only needed if you want to allow users to use your local mirror as a data source inside of Galaxy. If you don't want users to be able to use your local mirror as a data source, which may have faster loading times or additional data loaded that does not exist in UCSC's public site, you can safely remove the entry from your tool_conf.xml file without affecting the ability for your users to send files for display. Thanks for using Galaxy, Dan On Feb 27, 2012, at 1:13 PM, Josh Nielsen wrote: One more thing while I'm at it. For clarification would only the first two steps I listed be sufficient to get the display at link in Galaxy? If so what is the benefit of the other steps (other than having an actual link to your local genome browser mirror in Galaxy)? There's nothing that ties my internalgb entry to the new tool_id I created is there? On Mon, Feb 27, 2012 at 11:58 AM, Josh Nielsen jniel...@hudsonalpha.com wrote: Hi Dan, Good catch sir! Genius! It is working now. The spacing was exactly the same to the eye in vi for all the entries, but once I did a 'set list' in vi to display formatting characters I saw that 'main' had the tab ^I characters but my 'internalgb' entry didn't. This must have happened because I did a visual copy with my cursor. Thank you. -Josh On Mon, Feb 27, 2012 at 11:09 AM, Daniel Blankenberg d...@bx.psu.edu wrote: Hi Josh, It sounds like you are really close to getting this to work. My first guess would be that there is an issue with the modified ucsc_build_sites.txt file. Can you check that the line you copied is tab delimited and not space delimited? Thanks for using Galaxy, Dan On Feb 27, 2012, at 11:46 AM, Josh Nielsen wrote: Hello all, I am having some trouble getting a display at link to my local UCSC Genome Browser mirror to show up under my Galaxy jobs for viewing, although I can get the link to the online UCSC GB to display. I followed the suggestions in the following thread but it has yielded no results yet: http://gmod.827538.n3.nabble.com/using-local-Genome-Browser-mirror-td1829290.html. Here's what I have tried: - I edited the [galaxy-dir]/tool-data/shared/ucsc/ucsc_build_sites.txt file and duplicated the 'main' UCSC entry but changed the new entry's name to 'internalgb' and changed the URL to point to our local GB with cgi-bin/hgTracks? at the end - I set ucsc_display_sites = internalgb in universe_wsgi.ini - I made a modified copy of [galaxy-dir]/tools/data_source/ucsc_tablebrowser.xml (named HAIB_ucsc_tablebrowser.xml) in the same directory as the other XML files and created a tool link on the left side of the Galaxy page for it by adding it to the tool_conf.xml file (which works fine: when I click on it it loads our local Genome Browser inside the central Galaxy window frame) - I edited the HAIB_ucsc_tablebrowser.xml file according to the recommendation in the thread above: I had to change the name and id of the tool in the new ucsc_tablebrowser.xml file, and keep the id the same for the param.toold_id.value as well. So I gave it a unique id (changed ucsc_table_direct1 to HAIB_table_direct1) but kept the tool_id value field the same as the original/main UCSC tablebrowser (ucsc_table_direct1). Then I put the new HAIB id for our local tablebrowser into universe_wsgi.ini under the tool runners section as HAIB_table_direct1 = local:/// - And of course I have restarted Galaxy after each change. Still after all of this I cannot see a display at link for bam other files from Galaxy for my local UCSC GB. When I change universe_wsgi.ini to have ucsc_display_sites = internalgb,main set (for both browsers) the online/main GB will have a display at link on Galaxy jobs but no link shows for my local browser mirror. I'm also a little fuzzy on the relation between the ucsc_build_sites.txt file and the *_ucsc_tablebrowser.xml files (if any). Any tips as to what I might be missing here? Thanks! Josh ___ 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/ ___ 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] Upload file local option no longer appears
Hi Jim, Admin only actions are accessed from under the Admin panel. Can you check that you are accessing the Library from under the Admin interface and not from under Shared Data? Thanks for using Galaxy, Dan On Feb 27, 2012, at 12:24 PM, James Vincent wrote: Hello, I have been upload files to data libraries using the local file option to give a list of system file paths. Upon restarting galaxy (because of server reboot) I no longer have that option. The universe file has not changed and contains this, as it always has: # Add an option to the library upload form which allows administrators to # upload a directory of files. library_import_dir = /mnt/4TB When attempting to upload data sets to a library the only options in the pulldown are Upload files and Import datasets from current history. I am logged in as the administrator. Am I missing something very obvious here? I can't seem to find what went wrong or changed. Thanks, Jim ___ 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/ ___ 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] Setting the output label based on input parameters?
We are also feeling the hurt of not being able to carry the input dataset names through a complex workflow. We are also very interested in a solution similar to what Dave Walton has proposed,. Dave, would it be possible to receive a copy of your modified code? Does it work when there are multiple inputs? Ideally we would keep the names of datasets that are run through complex workflows the same as the workflow progresses. Sample mix-ups are a common scare, and with the current default naming it is not far fetched to see someone accidentally associating the end result with a different sample number. Thanks much, Ann ___ 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/
[galaxy-dev] Weird VDF format header
Hi,While technically not a Galaxy (Dev) question, but I am running into a non-standard VCF header in the GATK UnifiedGenotyper output.I see##FORMAT=ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification" ##INFO=ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed" ##INFO=ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed" Where Number=G and Number=A which does not pass the VCF Validator filter...Anyone know what is going on here? I had to change it to actual numbers (as the format describes..)Where does this header come from in the first place? Is it some standard header?ThanksThon ___ 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/
