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.
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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?
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
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!
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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:
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
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
.
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
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
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;
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
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Thanks for the reply, Nate!
Cheers,
CL
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Thanks for the reply! I'll try that one. I'll come back if the problem
still persists.
Cheers,
CL
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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
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 $_;
}
Hi all,
Do the uploaded files in Galaxy get indexed or sorted already?
Cheers,
CL
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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
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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
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
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
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
Okay, we'll do that! Thanks for the help.
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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
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
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
Thank you, Greg. I'll see it right away.
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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.
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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
Can non-admin users also utilize the option using filepaths?
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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
Thank you all for the answers!
CL
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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
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
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.
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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
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
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
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
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
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
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