Re: [galaxy-dev] Question about compressed files
Thanks for the quick reply. I've already checked how to configure our Galaxy instance for FTP upload, but due to security reasons, I cannot use that option. I read the wiki for Data Libraries and found that uploading via filesystem path can be used for putting files with size greater than 2GB in Galaxy. Since the data is stored in the same place where our Galaxy is installed, choosing the link option in Upload via Filesystem path seemed good enough. Anyway, at least now I'm sure that Galaxy indeed accepts compressed files. Again, 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/
Re: [galaxy-dev] Question about compressed files
Thank you for explaining it further, Jeremy. We'll keep that in mind next time we use that method. Anyway, I'm sorry for this redundant post, but I'm getting an error every time I am uploading a file into a data library using my non-admin user account. Galaxy says that there is no valid file within the user directory. The file I am uploading is a .fq file. I've made the necessary changes in universe_wsgi.ini and gave the necessary permissions to my user account. What could be causing that error? Thanks again! CL ___ 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 compressed files
Hi all, My colleague tried to upload via filesystem path a file with an approximate size of 2GB. It was a compressed file (filename.fq.gz). No error was reported, so I thought everything went fine, but when he tried running a tool, the uploaded file did not show in the input dropdown. But when he tried again, this time using an uncompressed file, every thing worked well. Now to my question: by default, can Galaxy accept and use compressed files? Or do I have to change something in its configuration just to do so? Thanks for the help! CL ___ 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] Galaxy can't find valid files in user folder
Hi all, My apologies for reposting this, but I thought I ought have asked this in a separate thread instead of appending it to a previous message. Anyway, I was able to set up a folder for a user (in my case, my own non-admin user account). universe_wsgi.ini's been configured to allow users to utilize a data library. I've also created a library for my non-admin user account. When all was set, I tried uploading a file to the library. But Galaxy prompted me that the folder did not contain any valid files. I thought I provided the wrong path; I even thought I really did not put anything in the folder. But when I checked, every thing seemed fine. I'm really stumped. I've searched the mailing list and even the wiki, and unfortunately I was not able to find a decent answer. I changed the file extension to .fastq and I indicated that the file to be uploaded was a FASTQ one, as Jen has suggested. I still got the same error in the end. I've scanned the universe_wsgi.ini file to see if there's anything else that I needed to configure, but I found none. Thanks in advance for your help! CL ___ 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] Script not working in Galaxy
Thanks for the reply! Weird enough though, the problem went away before I read this message. Still, thanks for the reply. We could use it for future reference. ___ 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] Deleting non-.dat files from Galaxy database
Hi all, These are some of the data that I have generated via Galaxy while I was experimenting with it. dataset_186.dat.bam dataset_265_files dataset_222.dat.bam dataset_266_files d dataset_346.dat.stat dataset_194.dat.fai dataset_267_files dataset_346.dat.temp dataset_727.dat.stat dataset_272_files dataset_727.dat.temp dataset_150.dat.bam dataset_273_files Is there another way in Galaxy to delete these without having to directly manipulate the database? Thanks! CL ___ 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] Configuring Data Library Usage for Non-Admins
Hi again, I've already done what you guys have suggested, but when I tried uploading a file, I got this error: The directory some directory here contains no valid files I checked if I placed the right path and created the correct folder, and everything seems fine. The file is a FASTQ file (ending in .fq). What could be causing Galaxy to see the file as not valid for upload? Thanks for the help! ___ 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] Script not working in Galaxy
Hi all, I have integrated a script that runs rsem in Galaxy and the following is the .xml that shows it in Galaxy: tool id=sixthStep name=RESM description/description command interpreter=perlexec_rrsem.pl $input1 $input2 $input3 $output1 $output2 /command inputs param name=input1 format=fasta type=data label=Transcript from OASES/ param name=input2 format=fastq type=data label=Left read: / param name=input3 format=fastq type=data label=Right read: / /inputs outputs data name=output1 format=text / data name=output2 format=text / /outputs /tool And here is exec_rrsem.pl, the file that accepts the parameters and sets everything up: $genes = $ARGV[3]; $isoforms = $ARGV[4]; $trans = $ARGV[0]; $left = $ARGV[1]; $right = $ARGV[2]; $directory = /home/applications/galaxy-dist/tools/VELVET-OASES; $transcript = $directory/trans.fa; $left_read = $directory/left_read.fastq; $right_read = $directory/right_read.fastq; symlink $trans, $transcript; symlink $left, $left_read; symlink $right, $right_read; @out #@out = `perl /home/applications/galaxy-dist/tools/VELVET-OASES/ run_rsem.pl 21`; run_rsem.pl is the actual script that runs the rsem programs. I'm wondering though, why Galaxy isn't executing the command properly. This is the same pattern I've used in other programs that I've integrated with Galaxy, so it came as a surprise to me when this one didn't run. Is there something wrong with my script? By the way, when I run exec_rrsem.pl from the konsole, it works just fine. Any insights on this? Thanks a lot! CL ___ 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] Configuring Data Library Usage for Non-Admins
Thank you all for the answers! CL ___ 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] Do input and output files get modified in Galaxy?
Hi all, This is going to be a very long message, so please bear with me. Anyway... I have been asked by my colleagues to integrate modified versions of velveth, velvetg and oases into our Galaxy instance. Of course, the first step was to upload the would-be input files. Since these are stored as .dat files in the database/files/000 folder, I symlinked the uploads to another folder. When I run the commands of the aforementioned steps, they access these symlinked files and perform the needed operations using them. I then just copy the data from the generated files onto the output files that would be visible in Galaxy. Is everything still clear? I hope so. Moving on... Now, they have asked me to integrate another script, and this time it is running rsem. It requires corrected left and right reads, and OASES' transcript output. But when I ran the rsem, I got an error concerning the input transcript file. I found two probable reasons why I was getting an error. One was that the transcript file might be empty. I've already checked this, and the file was not empty. Another reason was that the transcript FASTA file might not be following the required format. And so we arrive at my question: Do input and output files go through some minor format modifications when used in Galaxy? I have already manually ran the above commands, and everything works well. But when I downloaded the transcript file from Galaxy to use it via the konsole, I got the same error. Thank you in advance for any help, CL ___ 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] Configuring Data Library Usage for Non-Admins
Okay, so the only way for a user to upload a file with a size greater than 2GB is to use FTP? Or can a non-admin user be granted permission to upload files using the filesystem path option, given that he/she can only access his/her own directory? Thanks, CL ___ 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] Configuring Data Library Usage for Non-Admins
Hi all, I was able to configure Galaxy so that admins can use its Data Library functionality. My colleague then asked if I could do the same for non-admin users. I looked at the universe_wsgi.ini file and added a folder for the users. How will I know that all is ready? I logged-in with a non-admin account and I found nothing altered in the interface. Is there something else that I need to do? Thanks in advance for the help! Cheers, CL ___ 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] Configuring Data Library Usage for Non-Admins
Can non-admin users also utilize the option using filepaths? ___ 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] About the Galaxy Data Library
Thank you, Greg. I'll see it right away. ___ 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] Configuring Galaxy for FTP upload
Another question, Nate. After running Galaxy, I had problems with accessing the data in the created upload folder. Is there anything else that I need to do? Thank you so much for all the help. ___ 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] About the Galaxy Data Library
Hi all, I was checking out how to upload large files into Galaxy and I stumbled upon using Data Libraries. In the tutorial, I saw that the 'Create new data library sets' link has a dropdown next to it. When I ran our Galaxy instance, I found out that ours has none. Is that feature available only in the updated version of Galaxy, or could it be activated by changing something in the universe_wsgi.ini? Thanks in advance for any help, CL ___ 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] Configuring Galaxy for FTP upload
Hi all, So I was not able to configure Galaxy immediately after this post of mine due to the tasks that I first needed to do. Looking back, I forgot to ask this question: Do I need to perform the things stated in http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP? I just have set ftp_upload_dir to a created folder and ftp_upload_site to something other than None. Thanks in advance for the help! Cheers. CL ___ 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] About FTP Upload
Hi all, I checked basics.py after reading a similar post and saw this: self.ftp_upload_dir = kwargs.get( 'ftp_upload_dir', None ) self.ftp_upload_site = kwargs.get( 'ftp_upload_site', None ) Can you guys tell me what the None part means? Cheers, CL ___ 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] About Galaxy Configuration
Okay, we'll do that! Thanks for the help. ___ 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] About Galaxy Configuration
I didn't know that. Thanks for the reply! Now I have a new set of questions. First, how do I list myself as an admin? Should I just literally add my login detail in the config file? Second, my colleague would like to be able to edit and view the changes that he has made in his tools, even if I am doing some editing myself. Yesterday, he was running Galaxy and I was editing some tools. Since he has already started the instance, I got a socket error telling me that the address was already in use. Because of that, I was not able to see my revisions. What can we do about this? We're currently searching for ways on how Galaxy can handle 'multiusers'. Thanks again! On Thu, May 24, 2012 at 11:19 AM, Ross ross.laza...@gmail.com wrote: Hi, Ciara, AFAIK new tools always require a server restart at present, but an already loaded tool can have updates to the tool XML re-read using the 'Reload a tool's configuration' option from the administrative menu if your login is listed as an administrator in the config file. Restarting Galaxy seems relatively benign if jobs are running on a cluster. SGE jobs (eg) will be correctly handled and managed. Busy users may see a service unavailable message from Apache for the time it takes to restart but in my experience they can generally cope with the occasional unscheduled server bounce to import a new tool - YMMV On Thu, May 24, 2012 at 1:10 PM, Ciara Ledero lede...@gmail.com wrote: Hi there, I understand that everytime I create a new tool, I would have to restart Galaxy to see the changes that I've made. But if somebody else has already started Galaxy on our server, I won't be able to see my newly developed tool. I would be able to access the site, yes, but I won't see my tool. Is there a way around this? Cheers, CL ___ 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] Newbie question, adding a custom perl script
Hi there! Recently, I modified a Galaxy-intended velvet script so that the user would be able to put in his/her desired output directory ( the original script does not allow this). I just used a text box so as to ask for the output directory path (e.g. /home/galaxy/outputFolder). Then I just let Perl do the rest. Maybe in your case, you could just ask for the input and output directory paths. Then maybe you could just generate a text file that logs the end status of the process (i.e. whether it has been successful or not). This text file would be the one that shows up in your history. Cheers, CL Hi, A co-worker has a perl script that takes a directory path, and then interates over a the file in that directory and processes them into an output directory. I want to integrate that into galaxy. I've figured out that I'll need to create a tool XML conf with the inputs , outputs etc. My question is what param type should I use for a directory, in the input and output ? Or maybe what I'm looking for a is an input, output type that is a set of file (rather than tying it to a filesystem) Sorry for my beginners questions ! Thanks Mac ___ 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] Files not ending in .dat
Hi all, While I was checking Galaxy's database folder, I noticed that some of the files there did not end in .dat. For example, I had dataset_150.dat.bam, dataset_194.dat.fai and dataset_442_files. Can they be removed via the delete and purge scripts of Galaxy? Cheers, CL ___ 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] Accessing different folder's datasets
Hi all, I have just created scripts that ran velveth, velvetg and oases. The outputs of these commands are kept in a separate folder. Is it possible to show the data stored in this folder in our Galaxy web page? Or I don't have a choice but to upload them? Cheers, CL ___ 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] About the creation of a new folder
Hi all, I would just like to ask if it's possible to create a new folder (via script) in the galaxy-dist folder. Cheers, CL ___ 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] Empty file generation
This is my code for running samtools pileup:
open INP, $ARGV[0]
or die Cannot open file! $!;
open INP2, $ARGV[1]
or die Cannot open file! $!;
open OUT, $ARGV[2]
or die Cannot open file! $!;
open SCRIPT,samtools pileup -cv -f $ARGV[0] $ARGV[1] 2/dev/null | ;
while(SCRIPT) {
print OUT $_;
}
close INP;
close INP2;
close OUT;
close SCRIPT;
In the console, it works perfectly. But when run in Galaxy, it gives me an
empty file. I don't think it has something to do with the files that I am
using as input, for I just uploaded the ones that I used in the console
test-run. Any idea why this might be happening?
Cheers,
CL
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[galaxy-dev] Are uploads already indexed and/or sorted?
Hi all, Do the uploaded files in Galaxy get indexed or sorted already? Cheers, CL ___ 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] About pileups
Hi all, I am implementing a script in Galaxy that runs samtools' pileup command. Although it is running, I always get an empty file. I'm curious: what is the datatype of the output of a pileup/mpileup command? I think I might be having a problem with the output since the output data type might be incorrect. Thanks in advance for the help! Cheers, CL ___ 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] Configuring Galaxy for FTP upload
Thanks for the reply, Nate! Cheers, CL ___ 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] Unable to set BAM Metadata
Thanks for the reply! I'll try that one. I'll come back if the problem still persists. Cheers, CL ___ 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 set BAM Metadata
This is my code for running a samtools command internally, via Galaxy: open INP, $ARGV[0] or die Cannot open file: $!; $file = $ARGV[1]; open OUT, $file or die Cannot open file: $!; @out = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[0] 21`; print OUT @out; close INP; close OUT; The 21 is used to redirect the STDERR to STDOUT. When I run this in the console, it gives a non-empty file. But when run it in Galaxy, Galaxy can no longer find the path. This error message is given to me. Traceback (most recent call last): File /home/applications/galaxy-dist/lib/galaxy/jobs/runners/local.py, line 126, in run_job job_wrapper.finish( stdout, stderr ) File /home/applications/galaxy-dist/lib/galaxy/jobs/__init__.py, line 618, in finish dataset.set_meta( overwrite = False ) File /home/applications/galaxy-dist/lib/galaxy/model/__init__.py, line 874, in set_meta return self.datatype.set_meta( self, **kwd ) File /home/applications/galaxy-dist/lib/galaxy/datatypes/binary.py, line 179, in set_meta raise Exception, Error Setting BAM Metadata: %s % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: command not found The weird thing is, when I remove the 21 from the code and run it again in Galaxy, I am able to get this diagnostic message: [samopen] SAM header is present: 66338 sequences. This is the reason why I added the 21 in the first place, so that this diagnostic message would be 'ignored' (since it is detected as an error). Now, if the other code (the one without 21) is able to produce the aforementioned diagnostic message, then I assume that it is able to at least execute the samtools command internally. But when I add the 21, galaxy can no longer find the command. Do I need to specify a path somewhere in the galaxy-dist? I apologize for the very long message. Thanks in advance, CL ___ 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] What does this line of code mean
Hi all, Can I ask what this line of code does? job_wrapper.finish( stdout, stderr ) It's the one from the local.py. Cheers, CL ___ 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] About an additional tool
Hi all, This is what I did: $output = `/home/applications/samtools-0.1.7a/samtools view -bS $ARGV[0] * 21*`; The STDOUT was captured and redirected after I added the 21. Now, the result of the operation isn't in red. On Wed, Apr 25, 2012 at 8:44 AM, Ciara Ledero lede...@gmail.com wrote: To clear things up, I am using my own tool which uses samtools internally. I think I have tried the SAM-to-BAM tool when I was exploring Galaxy and I think it worked fine. By the way, I am using Perl. Thanks for the tips! I'll get back here if something goes awry again. CL On Wed, Apr 25, 2012 at 12:54 AM, Jim Johnson johns...@umn.edu wrote: * I put a samtools_filter tool in the toolshed that uses samtools view command. I called the samtools view command from the command section of the tool_config and redirected stderr to stdout to avoid having galaxy interpret it as an error. Jim Johnson Minnesota Supercomputing Institute University of Minnesota On Tue, Apr 24, 2012 at 10:03 AM, Ciara Ledero lede...@gmail.com lede...@gmail.com wrote: * *Hi there, I know? Galaxy already has a SAM-to-BAM converter, but part of my exercise/task is to incorporate a script that uses samtools' view command. I get this error: [samopen] SAM header is present: 66338 sequences. according to Galaxy. But this might not be an error at all. Is? there any way that I could tell Galaxy to ignore this and just continue with the script? Thanks in advance! Any help would be greatly appreciated. CL* ___ 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] About an additional tool
Hi there, I know Galaxy already has a SAM-to-BAM converter, but part of my exercise/task is to incorporate a script that uses samtools' view command. I get this error: [samopen] SAM header is present: 66338 sequences. according to Galaxy. But this might not be an error at all. Is there any way that I could tell Galaxy to ignore this and just continue with the script? Thanks in advance! Any help would be greatly appreciated. CL ___ 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] About an additional tool
To clear things up, I am using my own tool which uses samtools internally. I think I have tried the SAM-to-BAM tool when I was exploring Galaxy and I think it worked fine. By the way, I am using Perl. Thanks for the tips! I'll get back here if something goes awry again. CL On Wed, Apr 25, 2012 at 12:54 AM, Jim Johnson johns...@umn.edu wrote: * I put a samtools_filter tool in the toolshed that uses samtools view command. I called the samtools view command from the command section of the tool_config and redirected stderr to stdout to avoid having galaxy interpret it as an error. Jim Johnson Minnesota Supercomputing Institute University of Minnesota On Tue, Apr 24, 2012 at 10:03 AM, Ciara Ledero lede...@gmail.com lede...@gmail.com wrote: * *Hi there, I know? Galaxy already has a SAM-to-BAM converter, but part of my exercise/task is to incorporate a script that uses samtools' view command. I get this error: [samopen] SAM header is present: 66338 sequences. according to Galaxy. But this might not be an error at all. Is? there any way that I could tell Galaxy to ignore this and just continue with the script? Thanks in advance! Any help would be greatly appreciated. CL* ___ 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] Configuring Galaxy for FTP upload
Hi all, According to Galaxy, uploading files larger than 2GB will surely fail. For this reason, uploading via FTP is recommended. Unfortunately, I cannot download/install an FTP server for Galaxy since I am working on a remote server. I only have access to it via Xming. Is there anyway to allow FTP upload, without using ProFTPd? Can I use Mozilla's fireFTP or Linux's own FTP? (Actually, I tried to connect to Galaxy, but I was denied access.). Thank you in advance for any help. CL ___ 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] Deleting tmp files
Hi all, I would just like to ask if the tmp files in the galaxy-dist/database/tmp could be removed manually. Also, I ran into this error when I was purging my deleted datasets: Error attempting to purge data file: /home/applications/galaxy-dist/database/files/000/dataset_89.dat error: unsupported operand type(s) for -=: 'Decimal' and 'NoneType' What does that mean? I am new to Galaxy and to python, so I was a bit confused after seeing this error. The purging went on fine, though. The datasets have been removed from the database. Cheers, CL ___ 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] Manually removing datasets from database
Dear all, I was able to run the cleanup scripts in Galaxy, using the -r option with them. But why weren't the datasets removed from the disk? Can I now manually remove them? Cheers, Diana M. ___ 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] Manually deleting datasets from server
Dear all, I was able to execute the cleanup scripts in galaxy, using the -r option with them. According to what I've read, that option removes the datasets from the disk. But why didn't that happen? Also, since I have 'deleted and purged' the files, can I now remove them manually from the server? Cheers, CLedero ___ 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] Manually deleting datasets from server
Just an additional problem. I retried running the scripts, and I got this error when I was doing the purging: Removing disk, file Error attempting to purge data file: Traceback (most recent call last): File scripts/cleanup_datasets/cleanup_datasets.py, line 518, in module if __name__ == __main__: main() File scripts/cleanup_datasets/cleanup_datasets.py, line 116, in main purge_datasets( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry ) File scripts/cleanup_datasets/cleanup_datasets.py, line 353, in purge_datasets _purge_dataset( app, dataset, remove_from_disk, info_only = info_only ) File scripts/cleanup_datasets/cleanup_datasets.py, line 478, in _purge_dataset print Error attempting to purge data file: , dataset.file_name, error: , str( exc ) File /home/applications/galaxy-dist/lib/galaxy/model/__init__.py, line 651, in get_file_name assert self.object_store is not None, Object Store has not been initialized for dataset %s % self.id AssertionError: Object Store has not been initialized for dataset 1 Can you please enlighten me on this error? I am just new to Galaxy and Python, so I'm quite at a loss here. Thanks in advance for any help! On Fri, Apr 20, 2012 at 10:24 AM, Ciara Ledero lede...@gmail.com wrote: Dear all, I was able to execute the cleanup scripts in galaxy, using the -r option with them. According to what I've read, that option removes the datasets from the disk. But why didn't that happen? Also, since I have 'deleted and purged' the files, can I now remove them manually from the server? Cheers, CLedero ___ 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] cleanup_datasets.py inquiry
Hi all, I have tried Nate's fix on this script, but I got an indentation error in line 31. Any ideas on how to fix this? I'm not familiar with python, so I'm quite at a loss here. 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/
