Re: [galaxy-dev] [Galaxy-gcc2013] Strange behaviour with galaxy history
by Carl Eberhard
Hi, Ambrose
A couple of places to start:
Did the javascript console (in Firefox: Tools->Web Developer->Web
Console) display any errors when you reloaded the failing saved history
page?
What does is the output of 'hg summary' when run in a terminal from your
Galaxy root directory?
I believe you mentioned there were no 'ERROR' messages in the Galaxy log;
is this correct?
Thanks for the report. (I'm moving this to the galaxy-dev mailing list).
Carl
On Tue, Jul 2, 2013 at 3:50 PM, Ambrose Andongabo (RRes-Roth) <
Ambrose.Andongabo(a)rothamsted.ac.uk> wrote:
> Dear All,
>
> I updated my local galaxy instance yesterday and all my users cannot
> access their saved histories. When they click on saved histories all they
> get is an empty page. Checking the database, all the histories are there. I
> cleared the browser cache as many suggested but no luck yet. Any ideas of
> what can be done??
>
>
>
> Thanks
>
> Ambrose
>
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9 years, 7 months
Multiple output files do not appear in history
by Christoph Malisi
Hey,
I'm writing a XML for a tool that produces a number of output files. As the number is not known before the tool is run, I used the strategy outlined here:
http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Numbe...
First, I tried my tool definition in a galaxy instance in a virtual machine to not interrupt our production instance (we have a local instance set up). Here, everything worked fine. When trying the same code in our production galaxy instance, it didn't: Regardless of how many output files were produced, only one appears in the history. (the first one, corresponding to "output1" in the references wiki entry). When looking at the temp directory provided to the tool by galaxy ("$__new_file_dir__" in the wiki, it always points to "galaxy-dist/database/tmp/"), the additional output files have been created by my tool and are named correctly (e.g. primary_123_output2_visible_fastq, primary_123_output3_visible_fastq, …)
Both instances are new, based on release_2013.06.03.
Is there any setting in galaxy somewhere that could prevent this from working?
Thanks for your help
Chris
PS: I wrote a little python script that just creates multiple output files, and the discrepancy between the two instances is reproducible. Here is the code for the python script and the corresponding XML:
#######
import subprocess
import argparse
import os
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-i', type=int)
parser.add_argument('output1')
parser.add_argument('output1_id')
parser.add_argument('out_dir')
args = parser.parse_args()
print 'Wrapper arguments:', args
with open(args.output1, 'w') as f:
f.write('output1')
for i in range(2, args.i+1):
name = 'output%i'%i
file_type = 'text'
fname = '%s_%s_%s_%s_%s' % ('primary', args.output1_id, name, 'visible', file_type)
with open(os.path.join(args.out_dir, fname), 'w') as f:
f.write('output%i'%i)
if __name__ == "__main__":
main()
############################
###########################
<tool name="MultiOutTest" id="multiouttest">
<description>Multiple Outputs test</description>
<command interpreter="python">
multiout.py
-i $how_many
$output1
$output1.id
$__new_file_path__
</command>
<inputs>
<param name="how_many" type="integer" value="2" label="How many output files?"/>
</inputs>
<outputs>
<data name="output1" format="txt"/>
</outputs>
<help>
This is some help text.
</help>
</tool>
#################################
--
Dr. Christoph Malisi
Computomics GmbH & Co. KG
Sand 14 · 72076 Tübingen · Germany
http://computomics.com
9 years, 7 months
Error running tophat2 in Galaxy
by Sachit Adhikari
I am getting this error:
Error in tophat:
[2013-02-13 20:46:41] Beginning TopHat run (v2.0.7)
-----------------------------------------------
[2013-02-13 20:46:41] Checking for Bowtie
Bowtie version: 2.0.6.0
[2013-02-13 20:46:41] Checking for Samtools
Samtools version: 0.1.18.0
[2013-02-13 20:46:41] Checking for Bowtie index files
[2013-02-13 20:46:41] Checking for reference FASTA file
Warning: Could not find FASTA file
/data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa
[2013-02-13 20:46:41] Reconstituting reference FASTA file from Bowtie index
Executing: /usr/bin/bowtie2-inspect
/data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome >
./tophat_out/tmp/genome.fa
[2013-02-13 20:48:51] Generating SAM header for
/data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome
format: fastq
quality scale: phred33 (default)
[2013-02-13 20:49:23] Preparing reads
left reads: min. length=34, max. length=34, 2 kept reads (0 discarded)
Warning: you have only one segment per read.
If the read length is greater than or equal to 45bp,
we strongly recommend that you decrease --segment-length to about
half the read length because TopHat will work better with multiple
segments
[2013-02-13 20:49:23] Mapping left_kept_reads to genome genome with Bowtie2
[2013-02-13 20:49:56] Searching for junctions via segment mapping
Coverage-search algorithm is turned on, making this step very slow
Please try running TopHat again with the option
(--no-coverage-search) if this step takes too much time or memory.
Warning: junction database is empty!
[2013-02-13 20:51:18] Reporting output tracks
[FAILED]
Error running /usr/local/bin/tophat_reports --min-anchor 8
--splice-mismatches 0 --min-report-intron 50 --max-report-intron
500000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/
--max-multihits 20 --max-seg-multihits 40 --segment-length 25
--segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50
--max-closure-intron 5000 --min-coverage-intron 50
--max-coverage-intron 20000 --min-segment-intron 50
--max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2
--read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3
--max-deletion-length 3 -z gzip -p4 --no-closure-search
--no-microexon-search --sam-header
./tophat_out/tmp/genome_genome.bwt.samheader.sam
--report-discordant-pair-alignments --report-mixed-alignments
--samtools=/bin/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty
2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5
--bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5
--bowtie2-ref-gap-cont 3 ./tophat_out/tmp/genome.fa
./tophat_out/junctions.bed ./tophat_out/insertions.bed
./tophat_out/deletions.bed ./tophat_out/fusions.out
./tophat_out/tmp/accepted_hits ./tophat_out/tmp/left_kept_reads.bam
Loading ...done
What's wrong?
9 years, 7 months
Upload files to data library
by Lionel Guy
Hi!
I'm trying to upload multiple files a data library on my local instance
of Galaxy. I've looked at the tutorial on the Galaxy wiki
(http://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles),
where it's said that there are four options to upload files, available
by clicking the arrow at the top of the page one gets to when clicking
on the add dataset button.
However, although the tutorial shows the text "Create new data library
datasets" with an arrow next to it, the page I get to when clicking on
"Add datasets" shows "Upload files to a data library" with no arrow. I
thus cannot add files otherwise than by uploading files one by one.
Did I miss something? Am I doing anything wrong?
I'm using:
$ hg tip
changeset: 10003:b4a373d86c51
tag: tip
parent: 10001:471484ff8be6
Thanks for your help!
Lionel
Uppsala University
9 years, 7 months
Insert link in page editor
by Ted Goldstein
I want to make the page editor more useful.
This may be more a WYM editor question than a Galaxy question. But since Galaxy has its own enhanced WYM editor, I figure I would start here.
I was trying to use the galaxy page WYM editor today and I inserted a link (see image below). The behavior seems to put a wym guid as the text. I would have expected the title text prose from the dialogue box.
Can anyone comment on this? Why insert a weird non-user friendly WYM stamp guid?
Thanks,
Ted
9 years, 7 months
Strange Issue with Data Libraries
by Patel, Viren
Hello. After creating a data library and clicking on the 'Manage Data Libraries' menu to show the list of libraries, clicking on a data library name results in an "Unable to connect" message in Firefox, no action in Safari, and an "Error 102 (net::ERR_CONNECTION_REFUSED): The server refused the connection." when using Chrome. However, in all browsers, copying the link and pasting it into a new window works fine (the datasets/folders of the library are displayed and I can work with them normally). There are no messages in the Galaxy logs, web server logs, or system logs. Any insights to resolve this? Thanks.
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9 years, 7 months
Strange Issue with Data Library
by Patel, Viren
Hello. After creating a data library and clicking on the 'Manage Data Libraries' menu to show the list of libraries, clicking on a data library name results in an "Unable to connect" message in Firefox, no action in Safari, and an "Error 102 (net::ERR_CONNECTION_REFUSED): The server refused the connection." when using Chrome. However, in all browsers, copying the link and pasting it into a new window works fine (the datasets/folders of the library are displayed and I can work with them normally). There are no messages in the Galaxy logs, web server logs, or system logs. Any insights to resolve this? Thanks.
________________________________
This e-mail message (including any attachments) is for the sole use of
the intended recipient(s) and may contain confidential and privileged
information. If the reader of this message is not the intended
recipient, you are hereby notified that any dissemination, distribution
or copying of this message (including any attachments) is strictly
prohibited.
If you have received this message in error, please contact
the sender by reply e-mail message and destroy all copies of the
original message (including attachments).
9 years, 7 months
fastQ groomer waiting to run problem
by Xu, Ye
Hi there,
I am using Galaxy at BioCloud Central. I have successfully transferred total 30GB fastQ data from amazon S3 to galaxy. I tried to run fastQ groomer for each samples. But it said the job is waiting to run. I have waited a couple days and the job is still waiting. I called AWS, they told me my cluster working fine. So I don't know why the job can't start.
Thank you so much.
Best,
Ye Xu
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9 years, 7 months
