[galaxy-dev] Multiple file box in Galaxy XML
Hi all, I was wondering if it was possible for a user to specify the number of files to upload in Galaxy and have multiple file input boxes to upload updated on the wrapper page accordingly. A user will have from one to many files needed to be uploaded from a job. Right now I can see that galaxy does have the option for 1 file with the param file. With an options tagset, I can have the user specify a range. The easiest solution I can think of right now is to have a 1-N option tag set and create 1-N file upload boxes corresponding to the option number. Is there a better way already built in to Galaxy to do this? 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] Barcode Splitter: bug
Hi, I tried to use Barcode Splitter in Galaxy and could not get it work. In the Library to split pull down list, I could not get anything. I would expect it provides me information just like Barcodes to use pulldown list. Is this a bug? Yunling ___ 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] Question about from_work_dir
Hi everybody,
I'm currently trying to create a wrapper for one of my program.
This program generates several output file and the name of each output
file is derived from the name of the main input file.
_In the .xml file I try to get my output files with the following tag_:
outputs
data from_work_dir=${input_file}.out label=${input_file} main
output format=txt /
...
/outputs
_The corresponding input file tag_:
param name=input_file type=data label=Input label format=alr
help=Requested file type: ALR /
The problem is that the content of the from_work_dir attribute is not
interpreted by galaxy (Contrary to the label attribute) and therefore I
get this error message:
galaxy.jobs DEBUG 2011-11-28 17:44:24,431 finish(): Could not move
/home/galaxy/galaxy-dist/database/job_working_directory/326/${input_file}.out
to /home/galaxy/galaxy-dist/database/files/000/dataset_684.dat as
directed by from_work_dir
Do I made a syntax error ? Do I misunderstand the function of the
from_work_dir attribute?
Thank you in advance for your help.
Best regards,
Aurélien Bernard
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Re: [galaxy-dev] Question about from_work_dir
Aurelien,
The particular behavior that you need isn't currently supported because the
value of from_work_dir isn't treated as a template. To work around this
limitation, you can do the move/copy operations in your tool wrapper; see the
wrappers for Bowtie and Sicer for examples on how to do this.
Good luck,
J.
On Nov 28, 2011, at 12:21 PM, Aurélien Bernard wrote:
Hi everybody,
I'm currently trying to create a wrapper for one of my program.
This program generates several output file and the name of each output file
is derived from the name of the main input file.
In the .xml file I try to get my output files with the following tag:
outputs
data from_work_dir=${input_file}.out label=${input_file} main output
format=txt /
...
/outputs
The corresponding input file tag:
param name=input_file type=data label=Input label format=alr
help=Requested file type: ALR /
The problem is that the content of the from_work_dir attribute is not
interpreted by galaxy (Contrary to the label attribute) and therefore I get
this error message:
galaxy.jobs DEBUG 2011-11-28 17:44:24,431 finish(): Could not move
/home/galaxy/galaxy-dist/database/job_working_directory/326/${input_file}.out
to /home/galaxy/galaxy-dist/database/files/000/dataset_684.dat as directed by
from_work_dir
Do I made a syntax error ? Do I misunderstand the function of the
from_work_dir attribute ?
Thank you in advance for your help.
Best regards,
Aurélien Bernard
___
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and other Galaxy lists, please use the interface at:
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___
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Re: [galaxy-dev] [galaxy-user] Running shell script
On Nov 21, 2011, at 11:09 AM, Toqa Manasrah wrote: Hi everybody, I am integrating my software ViSpA inside galaxy and I have two questions: 1: the main program is a shell script (.sh) which call another shell script, which call Java executables. should I include any interpreter inside the .xml command tag? and what that should be? 2. how to guarantee that the output files destination are on the use local host rather than the server which is running galaxy? Hi Tuqa, Can you clarify this second question? I'm not sure what you're asking. Thanks, --nate Thanks and regards, Tuqa. ___ 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/ ___ 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] Can't view data files from published histories, only imported histories
Hi Jeremy, I'm trying to view boxplots (png) and FastQC (html) output. I can view other output types like tabular in the published histories, but not png or html. Thanks, Liisa Liisa Koski Bioinformatics Programmer Phone: 518-309-3079, E-Mail: liisa.ko...@dnalandmarks.ca Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec CANADA DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science company Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at supp...@dnalandmarks.ca.Confidentialité: L'information contenue dans ce courriel est confidentielle et peut être assujettie aux règles concernant le secret professionel. L'information contenue dans ce courriel est autorisée uniquement pour l'individu ou l'entité légale adressée. Si le récipiendaire ou le lecteur de ce message n'est pas celui ou celle prévue, vous êtes tenu de ne pas présenter, copier, distribuer ou utiliser le contenu de ce message. Si ce courriel est reçu par erreur, veuillez nous en excuser, veuillez détruire toutes copies de votre système nous informer à supp...@dnalandmarks.ca. From: Jeremy Goecks jeremy.goe...@emory.edu To: Liisa Koski liisa.ko...@dnalandmarks.ca Cc: galaxy-dev@lists.bx.psu.edu Date: 2011-11-28 13:23 Subject: Re: [galaxy-dev] Can't view data files from published histories, only imported histories Liisa, This functionality works fine in some instances, e.g. for this history: http://main.g2.bx.psu.edu/u/cartman/h/repeats I'd guess that it's related to the particular dataset type. What type of dataset are you trying to view when you see this error? Can you view any datasets from the history? Thanks, J. On Nov 28, 2011, at 1:11 PM, Liisa Koski wrote: Hi, I found a weird bug. I am trying to view data files by clicking on the 'eye' icon from a published history on my local galaxy installation. When I click on the eye I get a 'Server Error' and in the log file I get the following. Error - type 'exceptions.NameError': global name 'data' is not defined URL: http://domain:8080/u/user/d/8bdb720fee635874 File 'galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File 'galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File 'galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File 'galaxy_dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File 'galaxy_dist/lib/galaxy/web/controllers/dataset.py', line 693 in display_by_username_and_slug trans.response.set_content_type( data.get_mime() ) NameError: global name 'data' is not defined If I import the history into my own history pane I can click on the eye and see the data with no errors. Any ideas how I can see the data from the published histories? Thanks, Liisa Liisa Koski Bioinformatics Programmer ___ 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] [galaxy-user] Upload executable in galaxy
On Nov 23, 2011, at 11:10 AM, Giota Kottara wrote: Dear galaxy developers, I am trying to integrate an executable tool in a private instance of galaxy. I stored the configuration .xml file and the executable in tools folder of Galaxy and the tool appears in the homepage. Nevertheless when i am running the tool it doesn't seem to find the executable. Am I forgetting something? Hi Giota, I've moved this over to the galaxy-dev list since it pertains to tool development. Executables will need to be on the $PATH of the user running Galaxy. Could you share the error messages you receive when you run the tool? --nate Thank you in advance Giota Kottara ___ 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/ ___ 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] Error running tool
On Nov 25, 2011, at 8:23 AM, Toqa Manasrah wrote: Hello everybody, I am trying to run my tool Vispa but every time i try to i got this error messages: An error occurred running this job: /home/galaxy/galaxy-dist/tools/vispa/main.bash: line 13: ./parser_v.2.sh: No such file or directory /home/galaxy/galaxy-dist/tools/vispa/main.bash: line 16: ./vispa.bash: No such file or directory although all these files are reside under the same directory and have the permission 755. Hi Tuqa, The working directory used to execute your job is not the directory in which the tool itself resides. Your main script should use something like `basename $0` to determine what directory it's in, and then use that directory to call other scripts in the same directory. --nate how can I solve the problem? Thanks and regards, Tuqa. ___ 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] Shogun Toolbox?
Dear List, I am new to developing for Galaxy and haven't found a good answer to this question yet. Does Galaxy Test Toolshed use or recognize Shogun Toolbox (http://www.shogun-toolbox.org/)? I'm considering writing a module for Galaxy, but the underlying Python code relies on Shogun, and I haven't seen a suppported 3rd party software list, so I can't tell if Galaxy would be able to run the module without my rewriting it not to depend on Shogun. Thank you, Kipper Fletez-Brant ___ 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] Shogun Toolbox?
Dear Kipper, We are running most of our tools with the help of Shogun toolbox. Just configure a recent version of Shogun toolbox to your local machine and add the python path to your program. By doing this you will be able to call shogun functionalities in your programs. (Depends on the configuring path you will be able to find the shared object file and main library files) Recent version of shogun can be find at ftp://shogun-toolbox.org/shogun/releases/1.0/sources/shogun-1.0.0.tar.bz2 HTH, Vipin Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany Dear List, I am new to developing for Galaxy and haven't found a good answer to this question yet. Does Galaxy Test Toolshed use or recognize Shogun Toolbox ( http://www.shogun-toolbox.org/)? I'm considering writing a module for Galaxy, but the underlying Python code relies on Shogun, and I haven't seen a suppported 3rd party software list, so I can't tell if Galaxy would be able to run the module without my rewriting it not to depend on Shogun. Thank you, Kipper Fletez-Brant ___ 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] Can't view data files from published histories, only imported histories
Liisa, I'm not able to reproduce your issue on our public server. For instance, here's a history that includes both FastQC output and a boxplot; both display correctly: http://main.g2.bx.psu.edu/u/jeremy/h/unnamed-history-2 (Note that I just committed a fix to galaxy-central so that the images in the FastQC output show up correctly.) Some questions that might help us figure out the problem: *can you reproduce your problem on a public Galaxy instance, such as main or test? *is your Galaxy instance up to date? *is there something unusual about the datasets that you're using, e.g. are they imported on non-standard in some way? J. On Nov 28, 2011, at 1:35 PM, Liisa Koski wrote: Hi Jeremy, I'm trying to view boxplots (png) and FastQC (html) output. I can view other output types like tabular in the published histories, but not png or html. Thanks, Liisa Liisa Koski Bioinformatics Programmer Phone: 518-309-3079, E-Mail: liisa.ko...@dnalandmarks.ca Postal Address: DNA LandMarks Inc, St-jean-sur-Richelieu, J3B 6X3 Québec CANADA DNA LandMarks - une compagnie de BASF Plant Science / a BASF Plant Science company Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at supp...@dnalandmarks.ca.Confidentialité: L'information contenue dans ce courriel est confidentielle et peut être assujettie aux règles concernant le secret professionel. L'information contenue dans ce courriel est autorisée uniquement pour l'individu ou l'entité légale adressée. Si le récipiendaire ou le lecteur de ce message n'est pas celui ou celle prévue, vous êtes tenu de ne pas présenter, copier, distribuer ou utiliser le contenu de ce message. Si ce courriel est reçu par erreur, veuillez nous en excuser, veuillez détruire toutes copies de votre système nous informer à supp...@dnalandmarks.ca. From: Jeremy Goecks jeremy.goe...@emory.edu To: Liisa Koski liisa.ko...@dnalandmarks.ca Cc: galaxy-dev@lists.bx.psu.edu Date: 2011-11-28 13:23 Subject: Re: [galaxy-dev] Can't view data files from published histories, only imported histories Liisa, This functionality works fine in some instances, e.g. for this history: http://main.g2.bx.psu.edu/u/cartman/h/repeats I'd guess that it's related to the particular dataset type. What type of dataset are you trying to view when you see this error? Can you view any datasets from the history? Thanks, J. On Nov 28, 2011, at 1:11 PM, Liisa Koski wrote: Hi, I found a weird bug. I am trying to view data files by clicking on the 'eye' icon from a published history on my local galaxy installation. When I click on the eye I get a 'Server Error' and in the log file I get the following. Error - type 'exceptions.NameError': global name 'data' is not defined URL: http://domain:8080/u/user/d/8bdb720fee635874 File 'galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File 'galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File 'galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File 'galaxy_dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File 'galaxy_dist/lib/galaxy/web/controllers/dataset.py', line 693 in display_by_username_and_slug trans.response.set_content_type( data.get_mime() ) NameError: global name 'data' is not defined If I import the history into my own history pane I can click on the eye and see the data with no errors. Any ideas how I can see the data from the published histories? Thanks, Liisa Liisa Koski Bioinformatics Programmer ___ 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] Shogun Toolbox?
Hi Kipper, Sorry I got confused, Yes you are right, both ways are fine I think. --Vipin Vipin, Thanks for quick reply. Pardon my asking, as I said I am new to Galaxy development, but if I wanted to share my module, would other users need to install Shogun separately, or could I include it as a dependency or 'egg'? On Nov 28, 2011, at 2:28 PM, Vipin TS vipin...@gmail.com wrote: Dear Kipper, We are running most of our tools with the help of Shogun toolbox. Just configure a recent version of Shogun toolbox to your local machine and add the python path to your program. By doing this you will be able to call shogun functionalities in your programs. (Depends on the configuring path you will be able to find the shared object file and main library files) Recent version of shogun can be find at ftp://shogun-toolbox.org/shogun/releases/1.0/sources/shogun-1.0.0.tar.bz2 HTH, Vipin Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany Dear List, I am new to developing for Galaxy and haven't found a good answer to this question yet. Does Galaxy Test Toolshed use or recognize Shogun Toolbox ( http://www.shogun-toolbox.org/)? I'm considering writing a module for Galaxy, but the underlying Python code relies on Shogun, and I haven't seen a suppported 3rd party software list, so I can't tell if Galaxy would be able to run the module without my rewriting it not to depend on Shogun. Thank you, Kipper Fletez-Brant ___ 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] only showing first lines of large output file
hi matthias, i've also been getting metadata errors (below) for several weeks, but it works with the set_metadata_externally option (in the universe config file) set to False. for large files, it could take many minutes for your job server to check the metadata, and no new jobs will be run or completed jobs picked up during this delay, but at least it works reliably. fyi, the time these errors appeared roughly coincided with when i moved the data files (database/) to a different disk than the galaxy code. i don't know for sure if that's the issue or not, but may be a clue; i will experiment when i get a chance. galaxy.datatypes.metadata DEBUG 2011-11-28 12:39:01,129 setting metadata externally failed for Hist oryDatasetAssociation 449: External set_meta() not called galaxy.jobs DEBUG 2011-11-28 12:39:01,221 job 355 ended galaxy.datatypes.metadata DEBUG 2011-11-28 12:39:01,357 Cleaning up external metadata files galaxy.datatypes.metadata DEBUG 2011-11-28 12:39:01,496 Failed to cleanup MetadataTempFile temp fil es from ../../../groupdirs/Galaxy/dev/database/tmp/metadata_out_HistoryDatasetAssociation_449_sB_cT B: No JSON object could be decoded: line 1 column 0 (char 0) On Wed, Nov 16, 2011 at 3:00 AM, Mattias de Hollander m.dehollan...@nioo.knaw.nl wrote: ** Hello, I just noticed I get metadata errors in the paster.log file. Can someone tell me what they are and if they are related to above problem? galaxy.jobs.runners.drmaa DEBUG 2011-11-16 11:55:28,037 (840/588) state change: job finished normally galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:28,231 setting metadata externally failed for HistoryDatasetAssociation 1680: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_in_HistoryDatasetAssociation_1680_N7JVtq' galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:28,325 setting metadata externally failed for HistoryDatasetAssociation 1679: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_in_HistoryDatasetAssociation_1679_oTzTG_' galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:28,634 setting metadata externally failed for HistoryDatasetAssociation 1678: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_in_HistoryDatasetAssociation_1678_MgW15e'galaxy.jobs DEBUG 2011-11-16 11:55:29,103 job 840 ended galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:29,103 Cleaning up external metadata files galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:29,152 Failed to cleanup MetadataTempFile temp files from ../../galaxyData/tmp/metadata_out_HistoryDatasetAssociation_1678_UTGZz8: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_out_HistoryDatasetAssociation_1678_UTGZz8' galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:29,152 Failed to cleanup external metadata file (filename_in) for HistoryDatasetAssociation_1678: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_in_HistoryDatasetAssociation_1678_MgW15e' galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:29,152 Failed to cleanup external metadata file (filename_out) for HistoryDatasetAssociation_1678: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_out_HistoryDatasetAssociation_1678_UTGZz8' galaxy.datatypes.metadata DEBUG 2011-11-16 11:55:29,153 Failed to cleanup external metadata file (filename_kwds) for HistoryDatasetAssociation_1678: [Errno 2] No such file or directory: '../../galaxyData/tmp/metadata_kwds_HistoryDatasetAssociation_1678_3SDMLo' And of course, how to solve it :) Any help is appreciated. Mattias -- Bioinformatician Netherlands Institute of Ecology (NIOO-KNAW) Wageningen, the Netherlands ___ 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] Job output not returned from cluster
Ed, we had the classic goof on our cluster with this. 4 nodes could not see the /home/galaxy folder due to a missing entry in /etc/fstab. When the jobs hit those nodes (which explains the randomness) we got the error message. Bothersome was the lack of good logs to go on. The error message was too generic - however I discovered that Galaxy was depositing the error and our messages in the /pbs folder and you could briefly read them before they got deleted. There the message was the classic SGE input/output message - /home/galaxy file not found. Hence my follow up question - how can I have galaxy NOT to delete these SGE error and out files? best, joe From: Edward Kirton [eskir...@lbl.gov] Sent: Monday, November 28, 2011 4:15 PM To: Nate Coraor Cc: Joseph Hargitai; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Job output not returned from cluster hi, we've had this issue too -- in short, the cluster node(s) finish writing outfiles to disk, but the file system (inode metadata) isn't updated at the galaxy server yet when galaxy checks for the files. turning the metadata caching off (as recommended on the galaxy wiki) isn't an option for me (and the performance hit would be significant), so i added some loops around the file checking (5sec sleep and retry up to 6 times). there were a couple of places this probably should be done (not just .[eo]* log files but also the outfiles). i am testing these hacks now but due to the intermittent nature of these errors, it'll be a few days before i know if this is working as expected. once vetted, i will put these minor edits in a clone of galaxy-central so the changes can be picked up. ed On Mon, Oct 24, 2011 at 10:24 AM, Nate Coraor n...@bx.psu.edumailto:n...@bx.psu.edu wrote: Joseph Hargitai wrote: Nate, this error is intermittent. You resubmit the same job twice or three time and then it works. Once we are over the midterm exams - which use galaxy - we will try to switch the filesystem from autofs to hard mount. We suspect this to be the issue. Ah, I suspect this is attribute caching in NFS. Try mounting with the option 'noac' and see if it solves the problem. Could we suppress e and o SGE style to resolve this issue, or Galaxy wants the o? The filename is unimportant, but I doubt it's the cause. Do you have an idea about the url build for galaxy - ucsc page return when the url is :8080/galaxy and not just /galaxy? Not off the top of my head. I have this message marked, I'll take a look as soon as I have time. --nate thanks, joe From: Nate Coraor [n...@bx.psu.edumailto:n...@bx.psu.edu] Sent: Friday, October 21, 2011 10:26 AM To: Joseph Hargitai Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Job output not returned from cluster Joseph Hargitai wrote: Hi, i was browsing through the list and found many entries for this issue but not a definite answer. We are actually running into this error for simple file uploads from the internal filesystem. Hi Joe, This error occurs when the job's standard output and error files are not found where Galaxy expects them, namely: cluster_files_directory/job_id.o cluster_files_directory/job_id.e Please check your queueing system to make sure it can correctly deliver these back from the execution hosts to the specified filesystem. --nate thanks, joe ___ 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] Shogun Toolbox?
Vipin, Thanks for quick reply. Pardon my asking, as I said I am new to Galaxy development, but if I wanted to share my module, would other users need to install Shogun separately, or could I include it as a dependency or 'egg'? On Nov 28, 2011, at 2:28 PM, Vipin TS vipin...@gmail.com wrote: Dear Kipper, We are running most of our tools with the help of Shogun toolbox. Just configure a recent version of Shogun toolbox to your local machine and add the python path to your program. By doing this you will be able to call shogun functionalities in your programs. (Depends on the configuring path you will be able to find the shared object file and main library files) Recent version of shogun can be find at ftp://shogun-toolbox.org/shogun/releases/1.0/sources/shogun-1.0.0.tar.bz2 HTH, Vipin Friedrich Miescher Laboratory of the Max Planck Society Spemannstrasse 39, 72076 Tuebingen, Germany Dear List, I am new to developing for Galaxy and haven't found a good answer to this question yet. Does Galaxy Test Toolshed use or recognize Shogun Toolbox (http://www.shogun-toolbox.org/)? I'm considering writing a module for Galaxy, but the underlying Python code relies on Shogun, and I haven't seen a suppported 3rd party software list, so I can't tell if Galaxy would be able to run the module without my rewriting it not to depend on Shogun. Thank you, Kipper Fletez-Brant ___ 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/
