[galaxy-dev] Manually removing datasets from database

2012-04-19 Thread Ciara Ledero
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

[galaxy-dev] Manually deleting datasets from server

2012-04-19 Thread Ciara Ledero
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?

Re: [galaxy-dev] Manually deleting datasets from server

2012-04-19 Thread Ciara Ledero
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

[galaxy-dev] cleanup_datasets.py inquiry

2012-04-19 Thread Ciara Ledero
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

[galaxy-dev] Deleting tmp files

2012-04-20 Thread Ciara Ledero
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:

[galaxy-dev] Configuring Galaxy for FTP upload

2012-04-23 Thread Ciara Ledero
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

[galaxy-dev] About an additional tool

2012-04-24 Thread Ciara Ledero
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

Re: [galaxy-dev] About an additional tool

2012-04-24 Thread Ciara Ledero
. 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

Re: [galaxy-dev] About an additional tool

2012-04-25 Thread Ciara Ledero
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

[galaxy-dev] Unable to set BAM Metadata

2012-04-29 Thread Ciara Ledero
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;

[galaxy-dev] What does this line of code mean

2012-04-29 Thread Ciara Ledero
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

Re: [galaxy-dev] Configuring Galaxy for FTP upload

2012-05-01 Thread Ciara Ledero
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

2012-05-01 Thread Ciara Ledero
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,

[galaxy-dev] About pileups

2012-05-02 Thread Ciara Ledero
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

[galaxy-dev] Empty file generation

2012-05-03 Thread Ciara Ledero
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 $_; }

[galaxy-dev] Are uploads already indexed and/or sorted?

2012-05-03 Thread Ciara Ledero
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

[galaxy-dev] About the creation of a new folder

2012-05-10 Thread Ciara Ledero
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

[galaxy-dev] Accessing different folder's datasets

2012-05-15 Thread Ciara Ledero
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

[galaxy-dev] Files not ending in .dat

2012-05-21 Thread Ciara Ledero
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

[galaxy-dev] Newbie question, adding a custom perl script

2012-05-22 Thread Ciara Ledero
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

Re: [galaxy-dev] About Galaxy Configuration

2012-05-23 Thread Ciara Ledero
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

Re: [galaxy-dev] About Galaxy Configuration

2012-05-24 Thread Ciara Ledero
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] Configuring Galaxy for FTP upload

2012-06-10 Thread Ciara Ledero
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

[galaxy-dev] About FTP Upload

2012-06-10 Thread Ciara Ledero
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

[galaxy-dev] About the Galaxy Data Library

2012-06-11 Thread Ciara Ledero
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

Re: [galaxy-dev] About the Galaxy Data Library

2012-06-12 Thread Ciara Ledero
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

2012-06-12 Thread Ciara Ledero
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

[galaxy-dev] Configuring Data Library Usage for Non-Admins

2012-06-14 Thread Ciara Ledero
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

Re: [galaxy-dev] Configuring Data Library Usage for Non-Admins

2012-06-14 Thread Ciara Ledero
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:

Re: [galaxy-dev] Configuring Data Library Usage for Non-Admins

2012-06-18 Thread Ciara Ledero
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

Re: [galaxy-dev] Configuring Data Library Usage for Non-Admins

2012-06-20 Thread Ciara Ledero
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?

2012-06-20 Thread Ciara Ledero
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

[galaxy-dev] Script not working in Galaxy

2012-06-21 Thread Ciara Ledero
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

Re: [galaxy-dev] Script not working in Galaxy

2012-06-24 Thread Ciara Ledero
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.

[galaxy-dev] Deleting non-.dat files from Galaxy database

2012-06-24 Thread Ciara Ledero
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

Re: [galaxy-dev] Configuring Data Library Usage for Non-Admins

2012-06-24 Thread Ciara Ledero
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

[galaxy-dev] Galaxy can't find valid files in user folder

2012-07-02 Thread Ciara Ledero
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

[galaxy-dev] Question about compressed files

2012-07-03 Thread Ciara Ledero
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

Re: [galaxy-dev] Question about compressed files

2012-07-04 Thread Ciara Ledero
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

Re: [galaxy-dev] Question about compressed files

2012-07-04 Thread Ciara Ledero
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