Re: [galaxy-dev] Unnamed histories proliferating, can't get to my data
OK, we've made some progress. When we try to do uploads (or, I think, switch histories from the User->Saved Histories page), we get an error from get_history in /www/galaxy.hms.harvard.edu/support/galaxy-dist/lib/galaxy/web/framework/__ init__.py The code that makes it is: # Perhaps a bot is running a tool without having logged in to get a history log.debug( "Error: this request returned None from get_history(): %s" % self.request.browser_url ) So either self.galaxy_session.current_history is failing to return anything, or get_history is being called without create=False at the wrong time. Does this help narrow down what might be happening? It's not the FTP upload; this issue can happen with uploading through the browser, too. Thanks, -Amir Karger >On 10/23/12 2:42 PM, "Karger, Amir" wrote: > >>I'm using Galaxy from June, 2012. (Sorry if there's already a fix.) >> >>We've got it "working" in production. We've gotten whole pipelines to >>run. >>However, we occasionally get situations where we upload file (using the >>FTP mechanism), which seems to be fine, but then I can't get to the data. >>I went to Saved Histories, and selected Switch, and it outlined the line >>in blue and wrote "current history" next to it. But the right pane still >>shows "Unnamed history" with no data in it. Then if I go back to Saved >>Histories, I get one or two new Unnamed histories, created within the >>last >>few minutes. > > > ___ 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] Filter by quality error
I have a new workflow setup and filter by quality on an input fastqsanger file. I get the following error message where the original elements worked correctly. The IP address is a compute node. I have one compute node running with autoscaling on. Any reason why the mnt is working? /opt/sge/default/spool/execd/ip-10-140-4-84/job_scripts/39: line 13: /mnt/galaxyTools/tools/fastx_toolkit/0.0.13/env.sh: No such file or directory /opt/sge/default/spool/execd/ip-10-140-4-84/job_scripts/39: line 13: cd: /mnt/galaxyTools/galaxy-central: No such file or directory /opt/sge/default/spool/execd/ip-10-140-4-84/job_scripts/39: line 13: /mnt/galaxyTools/galaxy-central/set_metadata.sh: No such file or directory ___ 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] JBrowse direct export to Galaxy
> JBrowse is fully client-side, so there is no jbrowse server we can use. Is > there a way to pass data to galaxy directly without the server? This > functionality could also be useful for desktop applications. This isn't possible right now, though you could imagine using FTP with the API to achieve this. J.___ 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] Where should I put a tool's required binaries?
I installed the bedtools tool from the public toolshed to my galaxy cluster. The jobs were failing because I hadn't installed the required binaries: An error occurred running this job: /opt/sge/default/spool/execd/ip-10-194-50-118/job_scripts/2: line 13: genomeCoverageBed: command not found Taking a closer look at the toolshed's page, I noticed there were a handful of required binaries (genomeCoverageBed, intersectBed, etc). So I downloaded BEDTools and compiled all the binaries. I've put them in well organized directories using symlinks to specific versions, etc. The final executable directory containing symlinks to these binaries is "/mnt/galaxyTools/shed_tool_binaries/bin/". I can make a snapshot of the tools volume so that these compiled binaries are always available to me when I bring up my cluster, but how do I integrate them into the PATH in a way that lets the bedtools galaxy tool see them, but also survive cluster shutdowns? Thanks, -Joel ___ 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] Dynamic job runner status? Could I use it in combination with job splitting?
Hi, I've been researching the possibility of using dynamic job runner in combination with job splitting for blast jobs. My main interest is to create a rule where both the size of the query and the database are taken into consideration in order to select DRMAA and splitting options. My first question is what is the status on dynamic job runner? I found these two threads, but is not clear to me if this feature is part of galaxy-dist already: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-October/007160.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010080.html My second question is if there is any documentation other than the threads above to configure something like what I describe? In any case, there is very good information from John in these emails and I think that should get me started at least. Cheers, Carlos ___ 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] Empty TopHat output
Thanks, Jeremy. I updated my instance of Galaxy by the repository you provided ( https://bitbucket.org/galaxy/galaxy-dist/) and re-ran my analysis. I see that TopHat is generating data (by monitoring the disk usage on the Cloudman interface) again, but this time I the output file is in the error state and the message returned is: "Job output not returned from cluster". Any thoughts? Thanks in advance! Cheers, Mo Heydarian PhD candidate The Johns Hopkins School of Medicine Department of Biological Chemistry 725 Wolfe Street 414 Hunterian Baltimore, MD 21205 On Wed, Oct 31, 2012 at 9:03 PM, Jeremy Goecks wrote: > In this case, it's useful to differentiate between (i) the AMI that Galaxy > Cloud uses and (ii) the Galaxy code running on the cloud. I suspect that > (ii) is out of data for you; this is not (yet) automatically updated, even > when starting a new instance. > > Try using the admin console to update to the most recent Galaxy dist using > this URL: > > https://bitbucket.org/galaxy/galaxy-dist/ > > (not galaxy-central, as is the default) > > Best, > J. > > On Oct 31, 2012, at 8:36 PM, Mohammad Heydarian wrote: > > We are running "galaxy-cloudman-2011-03-22 (ami-da58aab3)". > > Our latest instance was loaded up just last week. > > Thanks! > > Cheers, > Mo Heydarian > > PhD candidate > The Johns Hopkins School of Medicine > Department of Biological Chemistry > 725 Wolfe Street > 414 Hunterian > Baltimore, MD 21205 > > > > On Wed, Oct 31, 2012 at 8:30 PM, Jeremy Goecks wrote: > >> Given that this doesn't seem to be happening on our public server or on >> local instances, my best guess is that the issue is old code. Are you >> running the most recent dist? >> >> J. >> >> >> On Oct 31, 2012, at 7:37 PM, Mohammad Heydarian wrote: >> >> We are still getting empty TopHat output files on our Galaxy instance on >> the cloud. We see that TopHat is generating data while the tool is running >> (by monitoring our disk usage on the Amazon cloud), but the output is >> "empty" files. >> >> Is anyone else having this issue? Does anyone have any suggestions? >> >> Many thanks in advance! >> >> >> Cheers, >> Mo Heydarian >> >> >> >> On Mon, Oct 15, 2012 at 4:53 AM, Joachim Jacob wrote: >> >>> The same here. >>> >>> Cheers, >>> Joachim >>> >>> -- >>> Joachim Jacob, PhD >>> >>> Rijvisschestraat 120, 9052 Zwijnaarde >>> Tel: +32 9 244.66.34 >>> Bioinformatics Training and Services (BITS) >>> http://www.bits.vib.be >>> @bitsatvib >>> >>> >>> __**_ >>> 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/ >> >> >> > > ___ 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] JBrowse direct export to Galaxy
I just noticed the part: "files_0|url_paste":
http://jbrowse-server.org/path/to/file.vcf";
JBrowse is fully client-side, so there is no jbrowse server we can use. Is
there a way to pass data to galaxy directly without the server? This
functionality could also be useful for desktop applications.
On Tue, Oct 23, 2012 at 9:59 PM, Brad Chapman wrote:
>
> Erik and Jeremy;
>
> >> I am a JBrowse Dev hoping to add the ability to export data directly
> >> from JBrowse (JavaScript) to Galaxy
> >
> > The API could be used for this.
> >
> > Specifically, you could do an upload for the user from a URL via the
> > tools API. I know that Brad Chapman (cc'd) has done this successfully
> > recently. Brad, can you share the parameters used to do this?
>
> Definitely, you want to do a POST to:
>
> /api/tools?key=YOURAPIKEY
>
> with a JSON payload of:
>
> {"tool_id": "upload1",
> "history_id": "identifier of history to use",
> "params": {"file_type": "vcf",
> "dbkey": "hg19",
> "files_0|url_paste":
> http://jbrowse-server.org/path/to/file.vcf";,
> "files_0|NAME": "file_name_for_history.vcf"}}
>
> This is all new since the last galaxy-dist release, so you'd need a
> recent galaxy-central server.
>
> Passing it back to Jeremy, there is also a Javascript wrapper around the
> tools API which might help:
>
>
> https://bitbucket.org/galaxy/galaxy-central/src/tip/static/scripts/mvc/tools.js
>
> but I haven't used it myself. Hope this helps,
> Brad
>
>
Thanks,
Erik Derohanian
___
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] hg18.fa on rsync? [was: which .loc file for "SAM to BAM"?]
Andreas, I recommend moving hg18.fa.fai into tool-data/shared/ucsc/hg18/sam_index/, and then samtools should work. Also, if you're using picard tools, you'll want hg18.fa.fai and hg18.dict in tool-data/shared/ucsc/hg18/srma_index/, as well as links to hg18.fa in both directories. --Dave B. On 11/1/12 11:59:24.000, Andreas Kuntzagk wrote: Dave, In the meantime I found that out by myself howto generate the FASTA and also to rum "samtools faidx" on it. The info about "all_fasta.loc" was missing. But it's still not working. Let me summarize what I did so far: - tool-data/shared/ucsc/hg18/seq/ contains these files: hg18.2bit hg18.fahg18.fa.fai where hg18.2bit was downloaded from the rsync server and the other two generated from it. - tool-data/shared/ucsc/builds.txt contains this line: hg18Human Mar. 2006 (NCBI36/hg18) (hg18) - tool-data/all_fasta.loc contains this line: hg18hg18Human (Homo sapiens): hg18 tool-data/shared/ucsc/hg18/seq/hg18.fa - tool-data/sam_fa_indices.loc contains this line: indexhg18tool-data/shared/ucsc/hg18/sam_index/hg18.fa - tool-data/srma_index.loc contains this line: hg18hg18hg18tool-data/shared/ucsc/hg18/srma_index/hg18.fa So any ideas where to look further? regards, Andreas On 01.11.2012 15:36, Dave Bouvier wrote: Andreas, When setting up the rsync server, we decided that .fa files would be excluded from the listing, since the 2bit format contains the same data but takes up to 75% less space. I would recommend downloading the relevant .2bit file and converting it back to FASTA with twoBitToFa, then updating your all_fasta.loc file to point to the resulting .fa file. --Dave B. On 11/1/12 06:27:49.000, Andreas Kuntzagk wrote: Hi, It's still not working. I just noticed that the sam_index dir only contains links to some files in ../seq which is mostly empty except some 2bit files. I could not find any documentation how to obtain these data files. regards, Andreas On 31.10.2012 17:50, Carlos Borroto wrote: On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk wrote: Hi, I'm still setting up a local galaxy. Currently I'm testing the setup of NGS tools. If I try "SAM to BAM" for a BAM file that has "hg18" set as build I get a message that "Sequences are not currently available for the specified build." I guess that I have either to manipulate one of the .loc files (but which?) or have to download additional data from rsync server. (I already have the tool-data/shared/hg18 completely) The .loc file you want to modify is 'tool-data/sam_fa_indices.loc'. You can find information about this subject in the wiki[1]. Although the table there is not complete, so you could always find the right xml under 'tools' and poke inside to find a line like this one: [1]http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup And I agree, dealing with .loc files is quite cumbersome. Hope it helps, Carlos ___ 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] Stop/Start/Reboot/Terminate
Dannon Thanks for the update. I was able to power through getting the EC2 instance to start using the cloud man interface in the same zone as the volume. Will let it run until next week. Amazon was not cooperating and kept launching instances in the opposite zone that I had the yaml file pointing to the storage volume. Finally got lucky after a couple attempts. Let me know if you want me to do any testing. Scooter On 11/1/12 11:20 AM, "Dannon Baker" wrote: >Galaxy Cloudman does not support Stop/Start through the AWS interface, >this is known to cause problems and should be avoided. The persistence >design allows for complete termination and restart -- the issue with your >startup zone can be worked around currently by launching through the AWS >console (following the instructions at usegalaxy.org/cloud) instead of >cloudlaunch. That said, I'm currently updating cloudlaunch to support >zone detection and launch, to avoid any issues with that moving forward, >but this won't be available on main until monday, most likely. > >That out of the way, the issue you're experiencing right now is likely >caused by an error with cm_boot.py causing duplicated nginx >max_client_body_size directives. > >This problem has been fixed on the back end and won't happen with any new >clusters going forward, but for existing clusters experiencing the >problem you can probably fix it in in a few short steps: > >ssh in to the instance >edit /opt/galaxy/pkg/nginx/conf/nginx.conf, removing any redundant >max_client_body_size directives. There should be exactly one in the file. >download a copy of the newest >https://s3.amazonaws.com/cloudman/cm_boot.py (save it to your desktop or >something) >In the AWS console, go to S3 and find your cluster's bucket (it'll have a >file called .clusterName, for easy identification. >Now upload the new cm_boot.py you just saved, replacing the one currently >in the bucket. > >Once the modified file is in your bucket, simply restart the instance via >the AWS console and everything *should* come up fine. > >Sorry for any inconvenience! > >-Dannon > > > >On Nov 1, 2012, at 10:49 AM, Scooter Willis wrote: > >> >> Last night I used the Amazon console to stop my working instance. Today >>started up the instance using amazon console. Waited appropriate time, >>using new assigned public ip address and no response. Also did a reboot >>and no response. I can ssh to the instance but do not know what to check >>for errors. >> >> Should you be able to stop/start and instance in amazon console and >>have it work correctly? Trying to avoid the "power down" option using >>the galaxy web interface since I had the problem with new instances >>being started in a different availability zone where the EBS volume was >>located. >> >> Looks like I will be leaving the master instance running and >>contributing to amazon profit margins! >> >> >> ___ >> 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] which .loc file for "SAM to BAM"?
Sorry for my unclear sentence, I meant the page you pointed me too. regards, Andreas On 01.11.2012 14:50, Carlos Borroto wrote: Well is not my page, I'm not directly related to Galaxy. Still, I think Galaxy Project would be happy to receive updates to the wiki, maybe a complete table can be added to the page you are mentioning. On Thu, Nov 1, 2012 at 4:27 AM, Andreas Kuntzagk wrote: Hi, thank you for the pointer. I was only looking at this wiki page: http://wiki.g2.bx.psu.edu/Admin/Data%20Integration Maybe this should point to your page? regards, Andreas On 31.10.2012 17:50, Carlos Borroto wrote: On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk wrote: Hi, I'm still setting up a local galaxy. Currently I'm testing the setup of NGS tools. If I try "SAM to BAM" for a BAM file that has "hg18" set as build I get a message that "Sequences are not currently available for the specified build." I guess that I have either to manipulate one of the .loc files (but which?) or have to download additional data from rsync server. (I already have the tool-data/shared/hg18 completely) The .loc file you want to modify is 'tool-data/sam_fa_indices.loc'. You can find information about this subject in the wiki[1]. Although the table there is not complete, so you could always find the right xml under 'tools' and poke inside to find a line like this one: [1]http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup And I agree, dealing with .loc files is quite cumbersome. Hope it helps, Carlos -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ 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] hg18.fa on rsync? [was: which .loc file for "SAM to BAM"?]
Dave, In the meantime I found that out by myself howto generate the FASTA and also to rum "samtools faidx" on it. The info about "all_fasta.loc" was missing. But it's still not working. Let me summarize what I did so far: - tool-data/shared/ucsc/hg18/seq/ contains these files: hg18.2bit hg18.fa hg18.fa.fai where hg18.2bit was downloaded from the rsync server and the other two generated from it. - tool-data/shared/ucsc/builds.txt contains this line: hg18Human Mar. 2006 (NCBI36/hg18) (hg18) - tool-data/all_fasta.loc contains this line: hg18hg18Human (Homo sapiens): hg18 tool-data/shared/ucsc/hg18/seq/hg18.fa - tool-data/sam_fa_indices.loc contains this line: index hg18tool-data/shared/ucsc/hg18/sam_index/hg18.fa - tool-data/srma_index.loc contains this line: hg18hg18hg18tool-data/shared/ucsc/hg18/srma_index/hg18.fa So any ideas where to look further? regards, Andreas On 01.11.2012 15:36, Dave Bouvier wrote: Andreas, When setting up the rsync server, we decided that .fa files would be excluded from the listing, since the 2bit format contains the same data but takes up to 75% less space. I would recommend downloading the relevant .2bit file and converting it back to FASTA with twoBitToFa, then updating your all_fasta.loc file to point to the resulting .fa file. --Dave B. On 11/1/12 06:27:49.000, Andreas Kuntzagk wrote: Hi, It's still not working. I just noticed that the sam_index dir only contains links to some files in ../seq which is mostly empty except some 2bit files. I could not find any documentation how to obtain these data files. regards, Andreas On 31.10.2012 17:50, Carlos Borroto wrote: On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk wrote: Hi, I'm still setting up a local galaxy. Currently I'm testing the setup of NGS tools. If I try "SAM to BAM" for a BAM file that has "hg18" set as build I get a message that "Sequences are not currently available for the specified build." I guess that I have either to manipulate one of the .loc files (but which?) or have to download additional data from rsync server. (I already have the tool-data/shared/hg18 completely) The .loc file you want to modify is 'tool-data/sam_fa_indices.loc'. You can find information about this subject in the wiki[1]. Although the table there is not complete, so you could always find the right xml under 'tools' and poke inside to find a line like this one: [1]http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup And I agree, dealing with .loc files is quite cumbersome. Hope it helps, Carlos ___ 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/ -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ 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] Stop/Start/Reboot/Terminate
Galaxy Cloudman does not support Stop/Start through the AWS interface, this is known to cause problems and should be avoided. The persistence design allows for complete termination and restart -- the issue with your startup zone can be worked around currently by launching through the AWS console (following the instructions at usegalaxy.org/cloud) instead of cloudlaunch. That said, I'm currently updating cloudlaunch to support zone detection and launch, to avoid any issues with that moving forward, but this won't be available on main until monday, most likely. That out of the way, the issue you're experiencing right now is likely caused by an error with cm_boot.py causing duplicated nginx max_client_body_size directives. This problem has been fixed on the back end and won't happen with any new clusters going forward, but for existing clusters experiencing the problem you can probably fix it in in a few short steps: ssh in to the instance edit /opt/galaxy/pkg/nginx/conf/nginx.conf, removing any redundant max_client_body_size directives. There should be exactly one in the file. download a copy of the newest https://s3.amazonaws.com/cloudman/cm_boot.py (save it to your desktop or something) In the AWS console, go to S3 and find your cluster's bucket (it'll have a file called .clusterName, for easy identification. Now upload the new cm_boot.py you just saved, replacing the one currently in the bucket. Once the modified file is in your bucket, simply restart the instance via the AWS console and everything *should* come up fine. Sorry for any inconvenience! -Dannon On Nov 1, 2012, at 10:49 AM, Scooter Willis wrote: > > Last night I used the Amazon console to stop my working instance. Today > started up the instance using amazon console. Waited appropriate time, using > new assigned public ip address and no response. Also did a reboot and no > response. I can ssh to the instance but do not know what to check for errors. > > Should you be able to stop/start and instance in amazon console and have it > work correctly? Trying to avoid the "power down" option using the galaxy web > interface since I had the problem with new instances being started in a > different availability zone where the EBS volume was located. > > Looks like I will be leaving the master instance running and contributing to > amazon profit margins! > > > ___ > 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] Unable to fetch the sequence ERROR
Hello, I am trying to fetch sequences using an interval file with columns 'chr', start, end and name. The names in the chr column are like chr1,chr2...chrY... and for the chrMT and the HSCHR*. I could fetch sequences for chr1-Y but it does not fetch for MT and HSCHR* and GL000*.1 I get the error "4536 warnings, 1st is: Unable to fetch the sequence from '33529672' to '329' for chrom 'HSCHR6_MHC_MCF'." Skipped 4536 invalid lines, 1st is #775, "HSCHR6_MHC_MCF 33529672 33530001 KIFC1". I locally cached the database as Human Hg19. Now does ur Hg19 contain MT and the other GL000*.1 and haplotype sequences in it ? Or do I change the headers of those lines in the interval file accordingly ? Id be glad if you could get back to me asap. Thanks ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Stop/Start/Reboot/Terminate
Last night I used the Amazon console to stop my working instance. Today started up the instance using amazon console. Waited appropriate time, using new assigned public ip address and no response. Also did a reboot and no response. I can ssh to the instance but do not know what to check for errors. Should you be able to stop/start and instance in amazon console and have it work correctly? Trying to avoid the "power down" option using the galaxy web interface since I had the problem with new instances being started in a different availability zone where the EBS volume was located. Looks like I will be leaving the master instance running and contributing to amazon profit margins! ___ 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] hg18.fa on rsync? [was: which .loc file for "SAM to BAM"?]
Andreas, When setting up the rsync server, we decided that .fa files would be excluded from the listing, since the 2bit format contains the same data but takes up to 75% less space. I would recommend downloading the relevant .2bit file and converting it back to FASTA with twoBitToFa, then updating your all_fasta.loc file to point to the resulting .fa file. --Dave B. On 11/1/12 06:27:49.000, Andreas Kuntzagk wrote: Hi, It's still not working. I just noticed that the sam_index dir only contains links to some files in ../seq which is mostly empty except some 2bit files. I could not find any documentation how to obtain these data files. regards, Andreas On 31.10.2012 17:50, Carlos Borroto wrote: On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk wrote: Hi, I'm still setting up a local galaxy. Currently I'm testing the setup of NGS tools. If I try "SAM to BAM" for a BAM file that has "hg18" set as build I get a message that "Sequences are not currently available for the specified build." I guess that I have either to manipulate one of the .loc files (but which?) or have to download additional data from rsync server. (I already have the tool-data/shared/hg18 completely) The .loc file you want to modify is 'tool-data/sam_fa_indices.loc'. You can find information about this subject in the wiki[1]. Although the table there is not complete, so you could always find the right xml under 'tools' and poke inside to find a line like this one: [1]http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup And I agree, dealing with .loc files is quite cumbersome. Hope it helps, Carlos ___ 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] which .loc file for "SAM to BAM"?
Well is not my page, I'm not directly related to Galaxy. Still, I think Galaxy Project would be happy to receive updates to the wiki, maybe a complete table can be added to the page you are mentioning. On Thu, Nov 1, 2012 at 4:27 AM, Andreas Kuntzagk wrote: > Hi, > > thank you for the pointer. > I was only looking at this wiki page: > http://wiki.g2.bx.psu.edu/Admin/Data%20Integration > > Maybe this should point to your page? > > regards, Andreas > > > On 31.10.2012 17:50, Carlos Borroto wrote: >> >> On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk >> wrote: >>> >>> Hi, >>> >>> I'm still setting up a local galaxy. Currently I'm testing the setup of >>> NGS >>> tools. If I try "SAM to BAM" for a BAM file that has "hg18" set as build >>> I >>> get a message that >>> "Sequences are not currently available for the specified build." I guess >>> that I have either to manipulate one of the .loc files (but which?) or >>> have >>> to download additional data from rsync server. >>> (I already have the tool-data/shared/hg18 completely) >>> >> >> The .loc file you want to modify is 'tool-data/sam_fa_indices.loc'. >> You can find information about this subject in the wiki[1]. Although >> the table there is not complete, so you could always find the right >> xml under 'tools' and poke inside to find a line like this one: >> > filename="sam_fa_indices.loc" metadata_name="dbkey" >> metadata_column="1" message="Sequences are not currently available for >> the specified build." line_startswith="index" /> >> >> [1]http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup >> >> And I agree, dealing with .loc files is quite cumbersome. >> >> Hope it helps, >> Carlos >> > > -- > Andreas Kuntzagk > > SystemAdministrator > > Berlin Institute for Medical Systems Biology at the > Max-Delbrueck-Center for Molecular Medicine > Robert-Roessle-Str. 10, 13125 Berlin, Germany > > http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ 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] hg18.fa on rsync? [was: which .loc file for "SAM to BAM"?]
Hi, It's still not working. I just noticed that the sam_index dir only contains links to some files in ../seq which is mostly empty except some 2bit files. I could not find any documentation how to obtain these data files. regards, Andreas On 31.10.2012 17:50, Carlos Borroto wrote: On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk wrote: Hi, I'm still setting up a local galaxy. Currently I'm testing the setup of NGS tools. If I try "SAM to BAM" for a BAM file that has "hg18" set as build I get a message that "Sequences are not currently available for the specified build." I guess that I have either to manipulate one of the .loc files (but which?) or have to download additional data from rsync server. (I already have the tool-data/shared/hg18 completely) The .loc file you want to modify is 'tool-data/sam_fa_indices.loc'. You can find information about this subject in the wiki[1]. Although the table there is not complete, so you could always find the right xml under 'tools' and poke inside to find a line like this one: [1]http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup And I agree, dealing with .loc files is quite cumbersome. Hope it helps, Carlos -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ 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] Parallelism tag and job splitter
On Thu, Nov 1, 2012 at 1:48 AM, Edward Hills wrote: > Hi Peter, thanks again. > > Turns out that it has been implemented by the looks of it in > lib/galaxy/datatypes/tabular.py under class Vcf. Yes, looking at the Vcf class it lacks a merge method (the Sam class earlier in the file defines its own - do something similar). > However, despite this, it > is always the Text class in data.py that is loaded and not the proper Vcf > one. Python inheritance means if the Vcf class it lacks a merge method, it would call the parent class' method (the Tabular class, if it had one), or the grandparent class's method (the Text class). So it is falling back on the Text merge which doesn't know about headers. (As an aside, I would like the Tabular merge to be a bit more clever about #header lines, but this isn't trivial as some tabular files contain #comment lines too.) > Can you point me in the direction of where the type is chosen? Your tool's XML should specify the output format - although there could be complications if for example you are doing a dynamic format selection based on one of the parameters. Peter ___ 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] which .loc file for "SAM to BAM"?
Hi, thank you for the pointer. I was only looking at this wiki page: http://wiki.g2.bx.psu.edu/Admin/Data%20Integration Maybe this should point to your page? regards, Andreas On 31.10.2012 17:50, Carlos Borroto wrote: On Wed, Oct 31, 2012 at 11:30 AM, Andreas Kuntzagk wrote: Hi, I'm still setting up a local galaxy. Currently I'm testing the setup of NGS tools. If I try "SAM to BAM" for a BAM file that has "hg18" set as build I get a message that "Sequences are not currently available for the specified build." I guess that I have either to manipulate one of the .loc files (but which?) or have to download additional data from rsync server. (I already have the tool-data/shared/hg18 completely) The .loc file you want to modify is 'tool-data/sam_fa_indices.loc'. You can find information about this subject in the wiki[1]. Although the table there is not complete, so you could always find the right xml under 'tools' and poke inside to find a line like this one: [1]http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup And I agree, dealing with .loc files is quite cumbersome. Hope it helps, Carlos -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ 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] Dataset upload fail
Hi Vladimir On 11/01/2012 03:46 AM, Vladimir Yamshchikov wrote: Local install of Galaxy on SciLinux55. Fails to upload 5.2 GB fastq file from local HD, while normally loading smaller fastq and fasta datasets (less than 1 GB). Chunks of 1.2 GB size remain in */database/tmp, which all represent beginning of the file that fails to upload. Several attempts to upload made and several chunks of the same size are present. Can I just copy the file dataset to database directory instead of uploading through web interface? Make sure you provide a directory for "library_import_dir" in the universe_wsgi.ini file. And copy your files to this location (or a sub directory of it). This will give you an extra option in the admin menu: 'Upload directory of files' and then use the 'Link files without copying to Galaxy' option. Alternatively, set "allow_library_path_paste" to 'True' (see also the comments and warnings in the universe_wsgi.ini file ) Regards, Hans-Rudolf ___ 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/
