Re: [galaxy-user] Cuffdiff Question
Hello Kurinji, I was at your USC Galaxy seminar last week, which I found very helpful - thank you! Glad to hear that you found the workshop helpful. As a reminder, please email questions about using Galaxy and its tools to the galaxy-user mailing list (which I've cc'd). You may get quicker and different responses from community members, and everyone will benefit from the discussion. I used my recently generated RNAseq data in Galaxy (which was pre-aligned using tophat and already had cufflinks run on it) - I ran cuffcompare with all the gtf files and then cuffdiff for the three pairs (there is 1 control and 3 different drug treatments - no replicates). I got several output files, as expected, but decided just to look at the gene differential expression as a start. Some questions I have are - 1. (very basic question!) which is sample 1 (and corresponding value 1) and sample 2 (and corresponding value 2)in my output file. This is what my output file is called - 90: Cuffdiff on data 37, data 38, and data 60: gene differential expression testing 33,969 lines Is 37 sample one or sample two? Given the data - I would expect sample 37 to correspond to value 2 - but I could be wrong. Please let me know! The best way to figure out which dataset corresponds with Cuffdiff's labels is to click the rerun button in the dataset: sample names correspond directly to the reads datasets (i.e. BAM files) provided as input to Cuffdiff. 2. How do I find the UCSC gene names corresponding with start/end sites - I did input the hg18 UCSC gtf file as a reference You'll need to use a reference annotation (GTF file) that has the gene_name attribute as input for Cufflinks/compare/difff. Typically Ensembl annotations have this attribute; however, you'll need to prepend 'chr' to each line--really, to each chromosome name--in order to bring Ensembl notation in line with UCSC/Galaxy notation. Actually, I noticed that value 1 in this particular output file is all 0 - no idea why. It is not this way in the other files, making me wonder if there is an error somewhere. I am sure the bam file is okay as I viewed it on IGV and saw the patterns I would expect for some candidate genes I looked at. It's difficult for me to comment without seeing your analysis. Some output files depend on particular attributes being set correctly in the annotation file. You may want to search through our mailing list archives and see if your question has already been answered: http://gmod.827538.n3.nabble.com/Galaxy-Users-f815892.html Good luck, J.___ 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/
[galaxy-user] SIFT analysis input and output file
Sometimes when I do a sift analysis, I noticed that the input and output alleles are different. I don't understand why and what does it means ? could you explain it to me ? For example, here you can see that the input allele is G/A for chr2 (first line) and the output is G/T * input file: chr2 230341630 + G/A chr2 43881517 + A/T chr10 115912482 - G/T chr10 115900918 - C/T * output file: #Chrom Position Strand Allele Codons Transcript IDProtein ID Substitution RegiondbSNP ID SNP Type Prediction Score Median Info Num seqs at position User Comment chr2230341630 + G/T -ENST0389045 ENSP0373697 NAEXON CDS rs1803846:A UnknownNot scored NA NA NA chr243881517 + A/T ATA-tTA ENST0260605 ENSP0260605 I230L EXON CDS rs11556157:T Nonsynonymous TOLERATED 0.47 3.19 7 chr10 115912482 + C/A CGA-CtA ENST0369285 ENSP0358291 R179L EXON CDS rs12782946:T Nonsynonymous TOLERATED 0.06 4.32 2 chr10 115900918 + G/A CAA-tAA ENST0369287 ENSP0358293 Q271* EXON CDS rs7095762:T Nonsynonymous N/A N/AN/A N/A Regards. Charlotte Gueydan -- *Charlotte Gueydan *, PhD. INSERM/Université Pierre et Marie Curie Hôpital Tenon - bâtiment de recherche 4, rue de la Chine 75020 Paris cedex 20 tel : 01 56 01 83 75 ___ 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/
[galaxy-user] cloud instance drops settings on reboot
Hi, setting the admin user in /mnt/galaxyTools/galaxy-central/universe_wsgi.ini did work after a simple restart of the galaxy service as user galaxy - ./runs.sh However, when I restarted the cloud instance (rebooted from Amazon console) the setting reverted to original. Is there perhaps another ini file that overrides this one on a reboot? Also, is there a proper/other way to restart the service? best, joe ___ 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/
Re: [galaxy-user] cloud instance drops settings on reboot
Hi Joe, This is by design. In order to change the settings in universe_wsgi.ini, you should edit file universe_wsgi.ini.cloud in the cluster's bucket on S3. This file get pulled in by Cloudman each time an instance starts. As far as restarting Cloudman, there is a (new) Admin panel (link at top right of the Cloudman console page) that gives you an option to restart Cloudman (as well as individual application-level services). Let us know if you have any more questions, Enis On Tue, Jun 28, 2011 at 11:29 AM, Joseph Hargitai joseph.hargi...@einstein.yu.edu wrote: Hi, setting the admin user in /mnt/galaxyTools/galaxy-central/universe_wsgi.ini did work after a simple restart of the galaxy service as user galaxy - ./runs.sh However, when I restarted the cloud instance (rebooted from Amazon console) the setting reverted to original. Is there perhaps another ini file that overrides this one on a reboot? Also, is there a proper/other way to restart the service? best, joe ___ 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/ ___ 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/
Re: [galaxy-user] SIFT analysis input and output file
Hello Charlotte, Would you be able to share a history containing your data run? Options - Share or Publish. Please email me the link and I will take a look. You can mail to me directly. Thank you, Jen Galaxy team On 6/28/11 8:08 AM, Charlotte Gueydan wrote: Sometimes when I do a sift analysis, I noticed that the input and output alleles are different. I don't understand why and what does it means ? could you explain it to me ? For example, here you can see that the input allele is G/A for chr2 (first line) and the output is G/T * input file: chr2 230341630 + G/A chr2 43881517 + A/T chr10 115912482 - G/T chr10 115900918 - C/T * output file: #Chrom Position Strand Allele Codons Transcript IDProtein ID Substitution RegiondbSNP ID SNP Type Prediction Score Median Info Num seqs at position User Comment chr2230341630 + G/T -ENST0389045 ENSP0373697 NAEXON CDS rs1803846:A UnknownNot scored NA NA NA chr243881517 + A/T ATA-tTA ENST0260605 ENSP0260605 I230L EXON CDS rs11556157:T Nonsynonymous TOLERATED 0.47 3.19 7 chr10 115912482 + C/A CGA-CtA ENST0369285 ENSP0358291 R179L EXON CDS rs12782946:T Nonsynonymous TOLERATED 0.06 4.32 2 chr10 115900918 + G/A CAA-tAA ENST0369287 ENSP0358293 Q271* EXON CDS rs7095762:T Nonsynonymous N/A N/AN/A N/A Regards. Charlotte Gueydan -- *Charlotte Gueydan *, PhD. INSERM/Université Pierre et Marie Curie Hôpital Tenon - bâtiment de recherche 4, rue de la Chine 75020 Paris cedex 20 tel : 01 56 01 83 75 ___ 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/ ___ 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/
Re: [galaxy-user] FTP and command line access in Galaxy
Peter Cock wrote: On Wed, Jun 22, 2011 at 6:47 AM, Robert Curtis Hendrickson curt...@uab.edu wrote: Nate, The Galaxy’s ability to pull files with user/password from FTP sites as a client is great. However, I need to pull data from an HTTP site at a sequencing center with user/password (already tried to get them to set up an FTP server, no luck). Any way to do this? Try asking the sequencing centre if the username and password can be provided as part of the HTTP URL, then give that URL to Galaxy. If it's using HTTP Authentication, the URL is the same as with ftp: http://user:h...@example.org/file.ext Other authentication systems which use forms and cookies or similar methods won't work. --nate Peter ___ 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/ ___ 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/
Re: [galaxy-user] cloud instance drops settings on reboot
Enis, thanks! I did edit the file in the bucket as much as adding an admin user. I uploaded the file back into the bucket but now the galaxy part is not starting. It is throwing an error: * 19:01:24 - Setting up Galaxy application * 19:01:24 - Retrieved file 'universe_wsgi.ini.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'. * 19:01:25 - Retrieved file 'tool_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/tool_conf.xml'. * 19:01:25 - Retrieved file 'tool_data_table_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/tool_data_table_conf.xml.cloud'. * 19:01:25 - Starting Galaxy... * 19:01:25 - Error invoking Galaxy, running command '/bin/su - galaxy -c export SGE_ROOT=/opt/sge; sh $GALAXY_HOME/run.sh --daemon' returned code '1' and following stderr: 'Traceback (most recent call last): File ./scripts/check_eggs.py, line 22, in c = Crate() File /mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py, line 259, in __init__ self.galaxy_config = GalaxyConfig() File /mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py, line 356, in __init__ if self.config.read( GalaxyConfig.config_file ) == []: File /usr/lib/python2.6/ConfigParser.py, line 286, in read self._read(fp, filename) File /usr/lib/python2.6/ConfigParser.py, line 482, in _read raise MissingSectionHeaderError(fpname, lineno, line) ConfigParser.MissingSectionHeaderError: File contains no section headers. file: /mnt/galaxyTools/galaxy-central/universe_wsgi.ini, line: 1 '\xff\xfe#\x00\n' Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 27, in c = Crate() File /mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py, line 259, in __init__ self.galaxy_config = GalaxyConfig() File /mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py, line 356, in __init__ if self.config.read( GalaxyConfig.config_file ) == []: File /usr/lib/python2.6/ConfigParser.py, line 286, in read self._read(fp, filename) File /usr/lib/python2.6/ConfigParser.py, line 482, in _read raise MissingSectionHeaderError(fpname, lineno, line) ConfigParser.MissingSectionHeaderError: File contains no section headers. file: /mnt/galaxyTools/galaxy-central/universe_wsgi.ini, line: 1 '\xff\xfe#\x00\n' ' Is the edited bucket file causing an issue? How do I get a new one or fix this? I did notice that the first uploaded try omitted the .cloud suffix, but i uploaded it again with the correct suffix. best, joe From: Enis Afgan [eaf...@emory.edu] Sent: Tuesday, June 28, 2011 11:46 AM To: Joseph Hargitai Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] cloud instance drops settings on reboot Hi Joe, This is by design. In order to change the settings in universe_wsgi.ini, you should edit file universe_wsgi.ini.cloud in the cluster's bucket on S3. This file get pulled in by Cloudman each time an instance starts. As far as restarting Cloudman, there is a (new) Admin panel (link at top right of the Cloudman console page) that gives you an option to restart Cloudman (as well as individual application-level services). Let us know if you have any more questions, Enis On Tue, Jun 28, 2011 at 11:29 AM, Joseph Hargitai joseph.hargi...@einstein.yu.edumailto:joseph.hargi...@einstein.yu.edu wrote: Hi, setting the admin user in /mnt/galaxyTools/galaxy-central/universe_wsgi.ini did work after a simple restart of the galaxy service as user galaxy - ./runs.sh However, when I restarted the cloud instance (rebooted from Amazon console) the setting reverted to original. Is there perhaps another ini file that overrides this one on a reboot? Also, is there a proper/other way to restart the service? best, joe ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.orghttp://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/ ___ 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:
Re: [galaxy-user] cloud instance drops settings on reboot
It seems that the formatting of the file was changed and Galaxy is unable to parse the file. The editor you used to edit the file might have done this once the file was saved. I'd suggest using vi to check the file and make sure it follows the formatting of universe_wsgi.ini.sample for example. Then, try uploading the file again. BTW, it's required for the file to have the .cloud extension. If all you're trying to do is add Galaxy admin users, the Cloudman Admin interface I mentioned earlier offers this functionality and it handles updating of the universe file. If you want to revert to what you had before, feel free to pull in the default universe_wsgi.ini.cloud file from 'cloudman' bucket on S3 and upload it to your cluster's bucket. Enis On Tue, Jun 28, 2011 at 3:21 PM, Joseph Hargitai joseph.hargi...@einstein.yu.edu wrote: Enis, thanks! I did edit the file in the bucket as much as adding an admin user. I uploaded the file back into the bucket but now the galaxy part is not starting. It is throwing an error: - 19:01:24 - Setting up Galaxy application - 19:01:24 - Retrieved file 'universe_wsgi.ini.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'. - 19:01:25 - Retrieved file 'tool_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/tool_conf.xml'. - 19:01:25 - Retrieved file 'tool_data_table_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/tool_data_table_conf.xml.cloud'. - 19:01:25 - Starting Galaxy... - 19:01:25 - Error invoking Galaxy, running command '/bin/su - galaxy -c export SGE_ROOT=/opt/sge; sh $GALAXY_HOME/run.sh --daemon' returned code '1' and following stderr: 'Traceback (most recent call last): File ./scripts/check_eggs.py, line 22, in c = Crate() File /mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py, line 259, in __init__ self.galaxy_config = GalaxyConfig() File /mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py, line 356, in __init__ if self.config.read( GalaxyConfig.config_file ) == []: File /usr/lib/python2.6/ConfigParser.py, line 286, in read self._read(fp, filename) File /usr/lib/python2.6/ConfigParser.py, line 482, in _read raise MissingSectionHeaderError(fpname, lineno, line) ConfigParser.MissingSectionHeaderError: File contains no section headers. file: /mnt/galaxyTools/galaxy-central/universe_wsgi.ini, line: 1 '\xff\xfe#\x00\n' Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 27, in c = Crate() File /mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py, line 259, in __init__ self.galaxy_config = GalaxyConfig() File /mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py, line 356, in __init__ if self.config.read( GalaxyConfig.config_file ) == []: File /usr/lib/python2.6/ConfigParser.py, line 286, in read self._read(fp, filename) File /usr/lib/python2.6/ConfigParser.py, line 482, in _read raise MissingSectionHeaderError(fpname, lineno, line) ConfigParser.MissingSectionHeaderError: File contains no section headers. file: /mnt/galaxyTools/galaxy-central/universe_wsgi.ini, line: 1 '\xff\xfe#\x00\n' ' Is the edited bucket file causing an issue? How do I get a new one or fix this? I did notice that the first uploaded try omitted the .cloud suffix, but i uploaded it again with the correct suffix. best, joe -- *From:* Enis Afgan [eaf...@emory.edu] *Sent:* Tuesday, June 28, 2011 11:46 AM *To:* Joseph Hargitai *Cc:* galaxy-user@lists.bx.psu.edu *Subject:* Re: [galaxy-user] cloud instance drops settings on reboot Hi Joe, This is by design. In order to change the settings in universe_wsgi.ini, you should edit file universe_wsgi.ini.cloud in the cluster's bucket on S3. This file get pulled in by Cloudman each time an instance starts. As far as restarting Cloudman, there is a (new) Admin panel (link at top right of the Cloudman console page) that gives you an option to restart Cloudman (as well as individual application-level services). Let us know if you have any more questions, Enis On Tue, Jun 28, 2011 at 11:29 AM, Joseph Hargitai joseph.hargi...@einstein.yu.edu wrote: Hi, setting the admin user in /mnt/galaxyTools/galaxy-central/universe_wsgi.ini did work after a simple restart of the galaxy service as user galaxy - ./runs.sh However, when I restarted the cloud instance (rebooted from Amazon console) the setting reverted to original. Is there perhaps another ini file that overrides this one on a reboot? Also, is there a proper/other way to restart the service? best, joe ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the
Re: [galaxy-user] cloud instance drops settings on reboot
Yeap, grabbed a new one from the tar file in the bucket and allowed Mac formatting to prevail. Unicode was the culprit. I am missing however the Cloudman Admin tab you are referring to. Is this a version issue? we use: galaxy-cloudman-2011-03-22 (ami-da58aab3) I do have the Admin tab in galaxy itself, but I do not think that is what you are referring to. joe From: Enis Afgan [eaf...@emory.edu] Sent: Tuesday, June 28, 2011 3:30 PM To: Joseph Hargitai Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] cloud instance drops settings on reboot It seems that the formatting of the file was changed and Galaxy is unable to parse the file. The editor you used to edit the file might have done this once the file was saved. I'd suggest using vi to check the file and make sure it follows the formatting of universe_wsgi.ini.sample for example. Then, try uploading the file again. BTW, it's required for the file to have the .cloud extension. If all you're trying to do is add Galaxy admin users, the Cloudman Admin interface I mentioned earlier offers this functionality and it handles updating of the universe file. If you want to revert to what you had before, feel free to pull in the default universe_wsgi.ini.cloud file from 'cloudman' bucket on S3 and upload it to your cluster's bucket. Enis On Tue, Jun 28, 2011 at 3:21 PM, Joseph Hargitai joseph.hargi...@einstein.yu.edumailto:joseph.hargi...@einstein.yu.edu wrote: Enis, thanks! I did edit the file in the bucket as much as adding an admin user. I uploaded the file back into the bucket but now the galaxy part is not starting. It is throwing an error: * 19:01:24 - Setting up Galaxy application * 19:01:24 - Retrieved file 'universe_wsgi.ini.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'. * 19:01:25 - Retrieved file 'tool_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/tool_conf.xml'. * 19:01:25 - Retrieved file 'tool_data_table_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/tool_data_table_conf.xml.cloud'. * 19:01:25 - Starting Galaxy... * 19:01:25 - Error invoking Galaxy, running command '/bin/su - galaxy -c export SGE_ROOT=/opt/sge; sh $GALAXY_HOME/run.sh --daemon' returned code '1' and following stderr: 'Traceback (most recent call last): File ./scripts/check_eggs.py, line 22, in c = Crate() File /mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py, line 259, in __init__ self.galaxy_config = GalaxyConfig() File /mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py, line 356, in __init__ if self.config.read( GalaxyConfig.config_file ) == []: File /usr/lib/python2.6/ConfigParser.py, line 286, in read self._read(fp, filename) File /usr/lib/python2.6/ConfigParser.py, line 482, in _read raise MissingSectionHeaderError(fpname, lineno, line) ConfigParser.MissingSectionHeaderError: File contains no section headers. file: /mnt/galaxyTools/galaxy-central/universe_wsgi.ini, line: 1 '\xff\xfe#\x00\n' Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 27, in c = Crate() File /mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py, line 259, in __init__ self.galaxy_config = GalaxyConfig() File /mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py, line 356, in __init__ if self.config.read( GalaxyConfig.config_file ) == []: File /usr/lib/python2.6/ConfigParser.py, line 286, in read self._read(fp, filename) File /usr/lib/python2.6/ConfigParser.py, line 482, in _read raise MissingSectionHeaderError(fpname, lineno, line) ConfigParser.MissingSectionHeaderError: File contains no section headers. file: /mnt/galaxyTools/galaxy-central/universe_wsgi.ini, line: 1 '\xff\xfe#\x00\n' ' Is the edited bucket file causing an issue? How do I get a new one or fix this? I did notice that the first uploaded try omitted the .cloud suffix, but i uploaded it again with the correct suffix. best, joe From: Enis Afgan [eaf...@emory.edumailto:eaf...@emory.edu] Sent: Tuesday, June 28, 2011 11:46 AM To: Joseph Hargitai Cc: galaxy-user@lists.bx.psu.edumailto:galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] cloud instance drops settings on reboot Hi Joe, This is by design. In order to change the settings in universe_wsgi.ini, you should edit file universe_wsgi.ini.cloud in the cluster's bucket on S3. This file get pulled in by Cloudman each time an instance starts. As far as restarting Cloudman, there is a (new) Admin panel (link at top right of the Cloudman console page) that gives you an option to restart Cloudman (as well as individual application-level services). Let us know if you have any more questions, Enis On Tue, Jun 28, 2011 at 11:29 AM, Joseph Hargitai
Re: [galaxy-user] cloud instance drops settings on reboot
The admin interface is something that I added just last week. It's not related to an AMI but to Cloudman itself. When was it you created the given cluster? If it's been in the last 5 days, the link should be there (take a look at the most recent newsbrief - there is a snapshot of the admin link interface there: https://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_06_23). If your cluster was older than that, Cloudman should have a option in the masthead to update it automatically. If you are to update, the link should show up. Let me know if neither is the case and we'll work on it more. Glad you got the configuration to work, Enis On Tue, Jun 28, 2011 at 3:45 PM, Joseph Hargitai joseph.hargi...@einstein.yu.edu wrote: Yeap, grabbed a new one from the tar file in the bucket and allowed Mac formatting to prevail. Unicode was the culprit. I am missing however the Cloudman Admin tab you are referring to. Is this a version issue? we use: galaxy-cloudman-2011-03-22 (ami-da58aab3) I do have the Admin tab in galaxy itself, but I do not think that is what you are referring to. joe -- *From:* Enis Afgan [eaf...@emory.edu] *Sent:* Tuesday, June 28, 2011 3:30 PM *To:* Joseph Hargitai *Cc:* galaxy-user@lists.bx.psu.edu *Subject:* Re: [galaxy-user] cloud instance drops settings on reboot It seems that the formatting of the file was changed and Galaxy is unable to parse the file. The editor you used to edit the file might have done this once the file was saved. I'd suggest using vi to check the file and make sure it follows the formatting of universe_wsgi.ini.sample for example. Then, try uploading the file again. BTW, it's required for the file to have the .cloud extension. If all you're trying to do is add Galaxy admin users, the Cloudman Admin interface I mentioned earlier offers this functionality and it handles updating of the universe file. If you want to revert to what you had before, feel free to pull in the default universe_wsgi.ini.cloud file from 'cloudman' bucket on S3 and upload it to your cluster's bucket. Enis On Tue, Jun 28, 2011 at 3:21 PM, Joseph Hargitai joseph.hargi...@einstein.yu.edu wrote: Enis, thanks! I did edit the file in the bucket as much as adding an admin user. I uploaded the file back into the bucket but now the galaxy part is not starting. It is throwing an error: - 19:01:24 - Setting up Galaxy application - 19:01:24 - Retrieved file 'universe_wsgi.ini.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'. - 19:01:25 - Retrieved file 'tool_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/tool_conf.xml'. - 19:01:25 - Retrieved file 'tool_data_table_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/tool_data_table_conf.xml.cloud'. - 19:01:25 - Starting Galaxy... - 19:01:25 - Error invoking Galaxy, running command '/bin/su - galaxy -c export SGE_ROOT=/opt/sge; sh $GALAXY_HOME/run.sh --daemon' returned code '1' and following stderr: 'Traceback (most recent call last): File ./scripts/check_eggs.py, line 22, in c = Crate() File /mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py, line 259, in __init__ self.galaxy_config = GalaxyConfig() File /mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py, line 356, in __init__ if self.config.read( GalaxyConfig.config_file ) == []: File /usr/lib/python2.6/ConfigParser.py, line 286, in read self._read(fp, filename) File /usr/lib/python2.6/ConfigParser.py, line 482, in _read raise MissingSectionHeaderError(fpname, lineno, line) ConfigParser.MissingSectionHeaderError: File contains no section headers. file: /mnt/galaxyTools/galaxy-central/universe_wsgi.ini, line: 1 '\xff\xfe#\x00\n' Traceback (most recent call last): File ./scripts/fetch_eggs.py, line 27, in c = Crate() File /mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py, line 259, in __init__ self.galaxy_config = GalaxyConfig() File /mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py, line 356, in __init__ if self.config.read( GalaxyConfig.config_file ) == []: File /usr/lib/python2.6/ConfigParser.py, line 286, in read self._read(fp, filename) File /usr/lib/python2.6/ConfigParser.py, line 482, in _read raise MissingSectionHeaderError(fpname, lineno, line) ConfigParser.MissingSectionHeaderError: File contains no section headers. file: /mnt/galaxyTools/galaxy-central/universe_wsgi.ini, line: 1 '\xff\xfe#\x00\n' ' Is the edited bucket file causing an issue? How do I get a new one or fix this? I did notice that the first uploaded try omitted the .cloud suffix, but i uploaded it again with the correct suffix. best, joe
Re: [galaxy-user] temporary files
Christopher Schroeder wrote: Dear all, we extended the galaxy functionality with a couple of smaller custom scripts. Now we are in the need of some tmpFiles, since our data is getting bigger. As far as I understand galaxy by now there might be several options: - job_working_directory (all normal files generated by the job, deleted upon completion of job - safe?) - tmp-folder within the database folder (custom path in universe_wsgi.ini?) - system-tmp-folder (e.g. samtools-wraper - only very limited space on this harddisk) What is the best way to store temporary data in Galaxy (that can be deleted after job completion)? Hi Chris, It's really up to your personal preference. In the past we've used all three. In general, if the filesystem your job_working_directory resides in is suitable, it is probably the easiest choice since you get free cleanup on job completion. --nate Thank you in advance for your help! Chris ___ 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/ ___ 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/
Re: [galaxy-user] Cuffdiff Question
Thanks for the reply. I tried to use the script provided on a previous galaxy thread for adding the chr on to the gtf file on the mac terminal but I keep getting this error - awk: can't open file ensembl.gtf source line number 1 I am very new to using the terminal so please let me know if there is something basic that I am not doing right, Try this Galaxy workflow: http://main.g2.bx.psu.edu/u/jeremy/w/make-ensembl-gtf-compatible-with-cufflinks It simply prepends 'chr' to the chromosome name, which is needed if you're using an Ensemble reference annotation and want to use it with Cufflinks/compare/diff in Galaxy. Best, J. ___ 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/
Re: [galaxy-user] cloud instance drops settings on reboot
Hi Oliver, A message in the masthead/top of the page main CloudMan console page offering to update CloudMan should show up automatically on page refresh when a version of CloudMan newer than the one currently running one exists in the default cloudman bucket. This functionality was added a few months ago now so if your instance is older, it won't work like that. In that case, it should be fine to manually download cm.tar.gz from 'cloudman' bucket and upload it to your cluster's bucket (replacing the current file there - although make a copy of the current file in case things don't work out as expected) and restart the instance. Enis On Tue, Jun 28, 2011 at 4:28 PM, Oliver Hofmann ohofm...@hsph.harvard.eduwrote: Enis, The admin interface is something that I added just last week. It's not related to an AMI but to Cloudman itself. When was it you created the given cluster? If it's been in the last 5 days, the link should be there (take a look at the most recent newsbrief - there is a snapshot of the admin link interface there: https://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_06_23). If your cluster was older than that, Cloudman should have a option in the masthead to update it automatically. If you are to update, the link should show up. Let me know if neither is the case and we'll work on it more. is there a way to update CloudMan through the older admin page as well (/cloud/admin)? It already has the Update Galaxy button and passes on the galaxy-central bitbucket URL to an 'update_galaxy' script, but doesn't seem to trigger anything beyond that (whether Galaxy itself is running or not). Best, Oliver Glad you got the configuration to work, Enis On Tue, Jun 28, 2011 at 3:45 PM, Joseph Hargitai joseph.hargi...@einstein.yu.edu wrote: Yeap, grabbed a new one from the tar file in the bucket and allowed Mac formatting to prevail. Unicode was the culprit. I am missing however the Cloudman Admin tab you are referring to. Is this a version issue? we use: galaxy-cloudman-2011-03-22 (ami-da58aab3) I do have the Admin tab in galaxy itself, but I do not think that is what you are referring to. joe From: Enis Afgan [eaf...@emory.edu] Sent: Tuesday, June 28, 2011 3:30 PM To: Joseph Hargitai Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] cloud instance drops settings on reboot It seems that the formatting of the file was changed and Galaxy is unable to parse the file. The editor you used to edit the file might have done this once the file was saved. I'd suggest using vi to check the file and make sure it follows the formatting of universe_wsgi.ini.sample for example. Then, try uploading the file again. BTW, it's required for the file to have the .cloud extension. If all you're trying to do is add Galaxy admin users, the Cloudman Admin interface I mentioned earlier offers this functionality and it handles updating of the universe file. If you want to revert to what you had before, feel free to pull in the default universe_wsgi.ini.cloud file from 'cloudman' bucket on S3 and upload it to your cluster's bucket. Enis On Tue, Jun 28, 2011 at 3:21 PM, Joseph Hargitai joseph.hargi...@einstein.yu.edu wrote: Enis, thanks! I did edit the file in the bucket as much as adding an admin user. I uploaded the file back into the bucket but now the galaxy part is not starting. It is throwing an error: • 19:01:24 - Setting up Galaxy application • 19:01:24 - Retrieved file 'universe_wsgi.ini.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/universe_wsgi.ini'. • 19:01:25 - Retrieved file 'tool_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/tool_conf.xml'. • 19:01:25 - Retrieved file 'tool_data_table_conf.xml.cloud' from bucket 'cm-99e0c68a2fe11e32a592e36abd1f2c38' to '/mnt/galaxyTools/galaxy-central/tool_data_table_conf.xml.cloud'. • 19:01:25 - Starting Galaxy... • 19:01:25 - Error invoking Galaxy, running command '/bin/su - galaxy -c export SGE_ROOT=/opt/sge; sh $GALAXY_HOME/run.sh --daemon' returned code '1' and following stderr: 'Traceback (most recent call last): File ./scripts/check_eggs.py, line 22, in c = Crate() File /mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py, line 259, in __init__ self.galaxy_config = GalaxyConfig() File /mnt/galaxyTools/galaxy-central/lib/galaxy/eggs/__init__.py, line 356, in __init__ if self.config.read( GalaxyConfig.config_file ) == []: File /usr/lib/python2.6/ConfigParser.py, line 286, in read self._read(fp, filename) File /usr/lib/python2.6/ConfigParser.py, line 482, in _read raise MissingSectionHeaderError(fpname, lineno, line) ConfigParser.MissingSectionHeaderError: File contains no section headers. file: /mnt/galaxyTools/galaxy-central/universe_wsgi.ini, line: 1
Re: [galaxy-user] cloud instance drops settings on reboot
throws this:
{updated: false}
From: Enis Afgan [eaf...@emory.edu]
Sent: Tuesday, June 28, 2011 6:02 PM
To: Oliver Hofmann; Joseph Hargitai
Cc: galaxy-user
Subject: Re: [galaxy-user] cloud instance drops settings on reboot
Well, now that I looked into it, about a week ago I did fix a bug with version
checking so that's probably why it's not triggering. To manually invoke the
update, you can paste this into your address bar and magic should happen :)
http://ec2-rest of ip/cloud/root/update_users_CM
Enis
P.S. Once the auto-checking is working, the attached screenshot shows what the
masthead is supposed to look like.
On Tue, Jun 28, 2011 at 5:25 PM, Oliver Hofmann
ohofm...@hsph.harvard.edumailto:ohofm...@hsph.harvard.edu wrote:
Enis,
running the default EC2 AMI (2011-03-22), cluster was started for the first
time about ten days ago so this is odd. I'll read up on how to manually update
CM.
Thanks!
Oliver
Hi Oliver,
A message in the masthead/top of the page main CloudMan console page
offering to update CloudMan should show up automatically on page refresh
when a version of CloudMan newer than the one currently running one
exists in the default cloudman bucket. This functionality was added a
few months ago now so if your instance is older, it won't work like
that. In that case, it should be fine to manually download cm.tar.gz
from 'cloudman' bucket and upload it to your cluster's bucket (replacing
the current file there - although make a copy of the current file in
case things don't work out as expected) and restart the instance.
Enis
On Tue, Jun 28, 2011 at 4:28 PM, Oliver Hofmann
ohofm...@hsph.harvard.edumailto:ohofm...@hsph.harvard.edu
mailto:ohofm...@hsph.harvard.edumailto:ohofm...@hsph.harvard.edu wrote:
Enis,
The admin interface is something that I added just last week.
It's not related to an AMI but to Cloudman itself. When was it you
created the given cluster? If it's been in the last 5 days, the link
should be there (take a look at the most recent newsbrief - there is
a snapshot of the admin link interface there:
https://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_06_23).
If your cluster was older than that, Cloudman should have a option
in the masthead to update it automatically. If you are to update,
the link should show up. Let me know if neither is the case and
we'll work on it more.
is there a way to update CloudMan through the older admin page as
well (/cloud/admin)? It already has the Update Galaxy button and
passes on the galaxy-central bitbucket URL to an 'update_galaxy'
script, but doesn't seem to trigger anything beyond that (whether
Galaxy itself is running or not).
Best, Oliver
Glad you got the configuration to work,
Enis
On Tue, Jun 28, 2011 at 3:45 PM, Joseph Hargitai
joseph.hargi...@einstein.yu.edumailto:joseph.hargi...@einstein.yu.edu
mailto:joseph.hargi...@einstein.yu.edumailto:joseph.hargi...@einstein.yu.edu
wrote:
Yeap,
grabbed a new one from the tar file in the bucket and allowed Mac
formatting to prevail. Unicode was the culprit.
I am missing however the Cloudman Admin tab you are referring to.
Is this a version issue?
we use: galaxy-cloudman-2011-03-22 (ami-da58aab3)
I do have the Admin tab in galaxy itself, but I do not think that
is what you are referring to.
joe
From: Enis Afgan [eaf...@emory.edumailto:eaf...@emory.edu
mailto:eaf...@emory.edumailto:eaf...@emory.edu]
Sent: Tuesday, June 28, 2011 3:30 PM
To: Joseph Hargitai
Cc: galaxy-user@lists.bx.psu.edumailto:galaxy-user@lists.bx.psu.edu
mailto:galaxy-user@lists.bx.psu.edumailto:galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] cloud instance drops settings on reboot
It seems that the formatting of the file was changed and Galaxy
is unable to parse the file. The editor you used to edit the file
might have done this once the file was saved. I'd suggest using vi
to check the file and make sure it follows the formatting of
universe_wsgi.ini.sample for example. Then, try uploading the file
again. BTW, it's required for the file to have the .cloud extension.
If all you're trying to do is add Galaxy admin users, the
Cloudman Admin interface I mentioned earlier offers this
functionality and it handles updating of the universe file. If you
want to revert to what you had before, feel free to pull in the
default universe_wsgi.ini.cloud file from 'cloudman' bucket on S3
and upload it to your cluster's bucket.
Enis
On Tue, Jun 28, 2011 at 3:21 PM, Joseph Hargitai
joseph.hargi...@einstein.yu.edumailto:joseph.hargi...@einstein.yu.edu
mailto:joseph.hargi...@einstein.yu.edumailto:joseph.hargi...@einstein.yu.edu
wrote:
Enis,
thanks! I did edit the file in the
Re: [galaxy-user] cloud instance drops settings on reboot
I apologize for making you go through multiple steps - when I sent my last
email, I looked at the controller code and not the actual method but it
turns out the method performs the same check as the UI, which fails, and so
does the method... Sorry.
Now, it's going to have to be done manually but it's quite straightforward.
So, just in case, make a copy of cm.tar.gz in your cluster's bucket. Then,
download cm.tar.gz from `cloudman` bucket and upload it to your cluster's
bucket. Then, in AWS S3 console, select the freshly uploaded file, click
Properties and then the Metadata tab. Add a new key value pair setting the
following to as the key `x-amz-meta-revision` and `114` as the value. Now,
restart the CloudMan instance and (less) magic should happen - but you
should have the most recent version of CloudMan running.
Hopefully this time it's going to happen :)
Thanks for patience.
Enis
On Tue, Jun 28, 2011 at 6:38 PM, Joseph Hargitai
joseph.hargi...@einstein.yu.edu wrote:
throws this:
{updated: false}
--
*From:* Enis Afgan [eaf...@emory.edu]
*Sent:* Tuesday, June 28, 2011 6:02 PM
*To:* Oliver Hofmann; Joseph Hargitai
*Cc:* galaxy-user
*Subject:* Re: [galaxy-user] cloud instance drops settings on reboot
Well, now that I looked into it, about a week ago I did fix a bug with
version checking so that's probably why it's not triggering. To manually
invoke the update, you can paste this into your address bar and magic should
happen :)
http://ec2-rest of ip/cloud/root/update_users_CM
Enis
P.S. Once the auto-checking is working, the attached screenshot shows
what the masthead is supposed to look like.
On Tue, Jun 28, 2011 at 5:25 PM, Oliver Hofmann ohofm...@hsph.harvard.edu
wrote:
Enis,
running the default EC2 AMI (2011-03-22), cluster was started for the
first time about ten days ago so this is odd. I'll read up on how to
manually update CM.
Thanks!
Oliver
Hi Oliver,
A message in the masthead/top of the page main CloudMan console page
offering to update CloudMan should show up automatically on page refresh
when a version of CloudMan newer than the one currently running one
exists in the default cloudman bucket. This functionality was added a
few months ago now so if your instance is older, it won't work like
that. In that case, it should be fine to manually download cm.tar.gz
from 'cloudman' bucket and upload it to your cluster's bucket (replacing
the current file there - although make a copy of the current file in
case things don't work out as expected) and restart the instance.
Enis
On Tue, Jun 28, 2011 at 4:28 PM, Oliver Hofmann
ohofm...@hsph.harvard.edu
mailto:ohofmann@hsph.harvard.**eduohofm...@hsph.harvard.edu
wrote:
Enis,
The admin interface is something that I added just last week.
It's not related to an AMI but to Cloudman itself. When was it you
created the given cluster? If it's been in the last 5 days, the link
should be there (take a look at the most recent newsbrief - there is
a snapshot of the admin link interface there:
https://bitbucket.org/galaxy/**galaxy-central/wiki/Features/**
DevNewsBrief/2011_06_23https://bitbucket.org/galaxy/galaxy-central/wiki/Features/DevNewsBrief/2011_06_23
).
If your cluster was older than that, Cloudman should have a option
in the masthead to update it automatically. If you are to update,
the link should show up. Let me know if neither is the case and
we'll work on it more.
is there a way to update CloudMan through the older admin page as
well (/cloud/admin)? It already has the Update Galaxy button and
passes on the galaxy-central bitbucket URL to an 'update_galaxy'
script, but doesn't seem to trigger anything beyond that (whether
Galaxy itself is running or not).
Best, Oliver
Glad you got the configuration to work,
Enis
On Tue, Jun 28, 2011 at 3:45 PM, Joseph Hargitai
joseph.hargi...@einstein.yu.**edu joseph.hargi...@einstein.yu.edu
mailto:joseph.hargitai@**einstein.yu.edujoseph.hargi...@einstein.yu.edu
wrote:
Yeap,
grabbed a new one from the tar file in the bucket and allowed Mac
formatting to prevail. Unicode was the culprit.
I am missing however the Cloudman Admin tab you are referring to.
Is this a version issue?
we use: galaxy-cloudman-2011-03-22 (ami-da58aab3)
I do have the Admin tab in galaxy itself, but I do not think that
is what you are referring to.
joe
From: Enis Afgan [eaf...@emory.edu mailto:eaf...@emory.edu]
Sent: Tuesday, June 28, 2011 3:30 PM
To: Joseph Hargitai
Cc: galaxy-user@lists.bx.psu.edu
mailto:galaxy-u...@lists.bx.**psu.edugalaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] cloud instance drops settings on reboot
It seems that the formatting of the file was changed and
Re: [galaxy-user] AXT and NIB files for AlignSeq.loc
Hello John, We do get these from UCSC when possible. Mouse sequence files (actually, all their browser files) are linked from their downloads page. As is the source code, which includes a set of pre-compiled utilities to convert between fasta - nib - 2bit, etc. http://genome.ucsc.edu and click on left side bar Downloads Hopefully this helps to get you set up, but if you need help with UCSC's tools, they may be the best contact: gen...@ucsc.edu. If you need more help with Galaxy's NGS set-up, please let us know, Best, Jen Galaxy team On 6/16/11 12:04 PM, John David Osborne wrote: I was wondering how to get a hold of the axt and/or nib files required by alignseq.loc. It's not mentioned on the local NGA Galaxy setup page. I was surprised to learn that: Fetch Sequences - Extract Genomic DNA requires AXT or NIB alignment files in order to extract mouse genomic DNA from BED file co-ordinates?! I see some AXT files at UCSC (a lot for human) but the alignment file I am guessing I needed (for this mm9 genome extraction) is mouse self? I'm hoping I don't have to generate them all myself, but if I do, I would love to know how to do it (parameters, etc...). Any info appreciated, -John ___ 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/ ___ 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/
Re: [galaxy-user] cloud instance drops settings on reboot
Enis,
thanks once again, works like a charm. Updated, the CloudMan interface
now has an admin page, and old data made it through the update.
Best,
Oliver
It's a publicly shared S3 bucket. You can download the file directly
through your browser too: http://s3.amazonaws.com/cloudman/cm.tar.gz
On Tue, Jun 28, 2011 at 7:03 PM, Joseph Hargitai
joseph.hargi...@einstein.yu.edu
mailto:joseph.hargi...@einstein.yu.edu wrote:
where do i find the 'cloudman' bucket?
j
*From:* Enis Afgan [eaf...@emory.edu mailto:eaf...@emory.edu]
*Sent:* Tuesday, June 28, 2011 6:48 PM
*To:* Joseph Hargitai
*Cc:* Oliver Hofmann; galaxy-user
*Subject:* Re: [galaxy-user] cloud instance drops settings on reboot
I apologize for making you go through multiple steps - when I sent
my last email, I looked at the controller code and not the actual
method but it turns out the method performs the same check as the
UI, which fails, and so does the method... Sorry.
Now, it's going to have to be done manually but it's quite
straightforward. So, just in case, make a copy of cm.tar.gz in your
cluster's bucket. Then, download cm.tar.gz from `cloudman` bucket
and upload it to your cluster's bucket. Then, in AWS S3 console,
select the freshly uploaded file, click Properties and then the
Metadata tab. Add a new key value pair setting the following to as
the key `x-amz-meta-revision` and `114` as the value. Now, restart
the CloudMan instance and (less) magic should happen - but you
should have the most recent version of CloudMan running.
Hopefully this time it's going to happen :)
Thanks for patience.
Enis
On Tue, Jun 28, 2011 at 6:38 PM, Joseph Hargitai
joseph.hargi...@einstein.yu.edu
mailto:joseph.hargi...@einstein.yu.edu wrote:
throws this:
{updated: false}
*From:* Enis Afgan [eaf...@emory.edu mailto:eaf...@emory.edu]
*Sent:* Tuesday, June 28, 2011 6:02 PM
*To:* Oliver Hofmann; Joseph Hargitai
*Cc:* galaxy-user
*Subject:* Re: [galaxy-user] cloud instance drops settings on reboot
Well, now that I looked into it, about a week ago I did fix a
bug with version checking so that's probably why it's not
triggering. To manually invoke the update, you can paste this
into your address bar and magic should happen :)
http://ec2-rest of ip/cloud/root/update_users_CM
Enis
P.S. Once the auto-checking is working, the attached screenshot
shows what the masthead is supposed to look like.
On Tue, Jun 28, 2011 at 5:25 PM, Oliver Hofmann
ohofm...@hsph.harvard.edu mailto:ohofm...@hsph.harvard.edu
wrote:
Enis,
running the default EC2 AMI (2011-03-22), cluster was
started for the first time about ten days ago so this is
odd. I'll read up on how to manually update CM.
Thanks!
Oliver
Hi Oliver,
A message in the masthead/top of the page main CloudMan
console page
offering to update CloudMan should show up automatically
on page refresh
when a version of CloudMan newer than the one currently
running one
exists in the default cloudman bucket. This
functionality was added a
few months ago now so if your instance is older, it
won't work like
that. In that case, it should be fine to manually
download cm.tar.gz
from 'cloudman' bucket and upload it to your cluster's
bucket (replacing
the current file there - although make a copy of the
current file in
case things don't work out as expected) and restart the
instance.
Enis
On Tue, Jun 28, 2011 at 4:28 PM, Oliver Hofmann
ohofm...@hsph.harvard.edu
mailto:ohofm...@hsph.harvard.edu
mailto:ohofmann@hsph.harvard.__edu
mailto:ohofm...@hsph.harvard.edu wrote:
Enis,
The admin interface is something that I added just
last week.
It's not related to an AMI but to Cloudman itself.
When was it you
created the given cluster? If it's been in the last
5 days, the link
should be there (take a look at the most recent
newsbrief - there is
a snapshot of the admin link interface there:
Re: [galaxy-user] cloud instance drops settings on reboot
same - looks nice and very useful.
best,
joe
From: Oliver Hofmann [ohofman...@gmail.com] on behalf of Oliver Hofmann
[ohofm...@hsph.harvard.edu]
Sent: Tuesday, June 28, 2011 7:29 PM
To: Enis Afgan
Cc: Joseph Hargitai; galaxy-user
Subject: Re: [galaxy-user] cloud instance drops settings on reboot
Enis,
thanks once again, works like a charm. Updated, the CloudMan interface
now has an admin page, and old data made it through the update.
Best,
Oliver
It's a publicly shared S3 bucket. You can download the file directly
through your browser too: http://s3.amazonaws.com/cloudman/cm.tar.gz
On Tue, Jun 28, 2011 at 7:03 PM, Joseph Hargitai
joseph.hargi...@einstein.yu.edu
mailto:joseph.hargi...@einstein.yu.edu wrote:
where do i find the 'cloudman' bucket?
j
*From:* Enis Afgan [eaf...@emory.edu mailto:eaf...@emory.edu]
*Sent:* Tuesday, June 28, 2011 6:48 PM
*To:* Joseph Hargitai
*Cc:* Oliver Hofmann; galaxy-user
*Subject:* Re: [galaxy-user] cloud instance drops settings on reboot
I apologize for making you go through multiple steps - when I sent
my last email, I looked at the controller code and not the actual
method but it turns out the method performs the same check as the
UI, which fails, and so does the method... Sorry.
Now, it's going to have to be done manually but it's quite
straightforward. So, just in case, make a copy of cm.tar.gz in your
cluster's bucket. Then, download cm.tar.gz from `cloudman` bucket
and upload it to your cluster's bucket. Then, in AWS S3 console,
select the freshly uploaded file, click Properties and then the
Metadata tab. Add a new key value pair setting the following to as
the key `x-amz-meta-revision` and `114` as the value. Now, restart
the CloudMan instance and (less) magic should happen - but you
should have the most recent version of CloudMan running.
Hopefully this time it's going to happen :)
Thanks for patience.
Enis
On Tue, Jun 28, 2011 at 6:38 PM, Joseph Hargitai
joseph.hargi...@einstein.yu.edu
mailto:joseph.hargi...@einstein.yu.edu wrote:
throws this:
{updated: false}
*From:* Enis Afgan [eaf...@emory.edu mailto:eaf...@emory.edu]
*Sent:* Tuesday, June 28, 2011 6:02 PM
*To:* Oliver Hofmann; Joseph Hargitai
*Cc:* galaxy-user
*Subject:* Re: [galaxy-user] cloud instance drops settings on reboot
Well, now that I looked into it, about a week ago I did fix a
bug with version checking so that's probably why it's not
triggering. To manually invoke the update, you can paste this
into your address bar and magic should happen :)
http://ec2-rest of ip/cloud/root/update_users_CM
Enis
P.S. Once the auto-checking is working, the attached screenshot
shows what the masthead is supposed to look like.
On Tue, Jun 28, 2011 at 5:25 PM, Oliver Hofmann
ohofm...@hsph.harvard.edu mailto:ohofm...@hsph.harvard.edu
wrote:
Enis,
running the default EC2 AMI (2011-03-22), cluster was
started for the first time about ten days ago so this is
odd. I'll read up on how to manually update CM.
Thanks!
Oliver
Hi Oliver,
A message in the masthead/top of the page main CloudMan
console page
offering to update CloudMan should show up automatically
on page refresh
when a version of CloudMan newer than the one currently
running one
exists in the default cloudman bucket. This
functionality was added a
few months ago now so if your instance is older, it
won't work like
that. In that case, it should be fine to manually
download cm.tar.gz
from 'cloudman' bucket and upload it to your cluster's
bucket (replacing
the current file there - although make a copy of the
current file in
case things don't work out as expected) and restart the
instance.
Enis
On Tue, Jun 28, 2011 at 4:28 PM, Oliver Hofmann
ohofm...@hsph.harvard.edu
mailto:ohofm...@hsph.harvard.edu
mailto:ohofmann@hsph.harvard.__edu
mailto:ohofm...@hsph.harvard.edu wrote:
Enis,
The admin interface is something that I added just
last week.
It's not
