Help with Summary Statistics
by D. A. Cowart
Hello,
I am attempting to use Galaxy to calculate the mean sequence read
length and identify the range of read lengths for my 454 data. The
data has already been organized and sorted by species. The format of
the data is as follows:
>HD4AU5D01BHBCQCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC
>HD4AU5D01A093MCTCTGTCGCTCTGTCTCTCTTCTCTCTCTCTCTCTCT
etc...for each species
I have attempted to use the "Summary Statistics" button, however it
appears to only be for numerical data and not sequence data. Is this
tool/task available
via Galaxy?
Thank you,
Dominique Cowart
User name: dac330
8 years, 4 months
SNP finding
by Xiefan Fang
Dear galaxy users,
We have done deep sequencing on some known genomic loci using
Hiseq2000. I have already mapped the reads to the reference sequences by
using Galaxy. In the next step, I want to find SNPs and calculate the SNP
percentage within the reads. There are 500,000 to 1,000,000 reads per
biological sample. Can I do it with galaxy? If not, is there other programs
available in windows? Considering that I am not very familiar with
programming.
Thanks,
Xiefan
University of Florida
8 years, 10 months
Why don't we get FPKMs from this gene?
by Dikla Aharonovich
Hello,
We are using BAM to map Illumina reads to a bacterial genome, followed by Cufflinks o get the FPKMs. We have come across many genes for which we get FPKM=0 (using both gene and transcript expression) even though there are reads mapping to these gene IDs (e.g. the region between the dashed lines in the attached screenshot). Can anyone suggest a reason/fix for this?
Thanks
Dikla
9 years, 6 months
Filter Pileup in SAM tools
by Andrew South
NGS: SAM Tools
I have generated a simple 6 column pileup from my BAM file but when I try to use the Filter Pileup tool it doesn't recognise my pileup file, I receive the message "History does not include a dataset of the required format / build". Build is hg19. Curiously in the same history I have ran the tool through a workflow without a hitch.
Any advice to successfully filter my pileup would be gratefully received.
Many thanks,
Andy
The University of Dundee is a registered Scottish Charity, No: SC015096
9 years, 7 months
Error / Nebula and RepeatMasker
by Sarah Maman
Hello,
I've installed NEBULA tools and "RepeatMasker" tool on our local Galaxy
instance.
For some tools (others work), I get the following errors:
* - *Here is the error I get when running the tool *FilterControl *
*** glibc detected *** java: double free or corruption (!prev): 0x00007fe56800ecd0 ***
*** glibc detected *** java: double free or corruption (!prev): 0x00007fe56800ecd0 ***
*** glibc detected *** java: double free or corruption (!prev): 0x00007fe56800ecd0 ***
*** glibc detected *** java: double free or corruption (!prev): 0x00007fe56800ecd0 ***
/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/FilterControlPeaks/FilterControlPeaks.sh: line 80: 61310 Abandon java -classpath $LOCAL_PATH/ -Xmx6g FilterPeaks -f $inputfile -c $controlfile -t $minHeight -v $minRatio -o $output > /dev/null
*** glibc detected *** java: double free or corruption (!prev): 0x00007f1f5800ecd0 ***
/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/FilterControlPeaks/FilterControlPeaks.sh: line 81: 61351 Abandon
- Here is the error I get when running the tool *IntersectBed
*//work/galaxy/database/pbs/galaxy_4129.sh: line 13: Erreur de syntaxe
près du symbole inattendu « ;; »
/work/galaxy/database/pbs/galaxy_4129.sh: line 13: `bedtools intersect
-f 0.05/
- Here is the error I get when running the tool *ChIPmunk (thanks Alban
for you help (*ChIPMunk v2 is used and all librairies are found) *but
here is a new error, maybe a problem of "dirname" ?)
*/mv: impossible d'évaluer
« /work/galaxy/database/job_working_directory/004/4132/galaxy_dataset_5992.dat_0.xml.png »:
Aucun fichier ou dossier de ce type
mv: impossible d'évaluer « /work/gala
/- Here is the error I get when running the tool *PeaksToBed
*
readline() on closed filehandle FILE at
/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl line 124 (#1)
(W closed) The filehandle you're reading from got itself closed sometime
before now. Check your control flow.
Use of uninitialized value $fields[1] in concatenation (.) or string at
/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl line 154, <FILE> line 1 (#2)
(W uninitialized) An undefined value was used as if it were already
defined. It was interpreted as a "" or a 0, but maybe it was a mistake.
To suppress this warning assign a defined value to your variables.
To help you figure out what was undefined, perl will try to tell you the
name of the variable (if any) that was undefined. In some cases it cannot
do this, so it also tells you what operation you used the undefined value
in. Note, however, that perl optimizes your program and the operation
displayed in the warning may not necessarily appear literally in your
program. For example, "that $foo" is usually optimized into "that "
. $foo, and the warning will refer to the concatenation (.) operator,
even though there is no . in your program.
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl line 154, <FILE> line 1 (#2)
Use of uninitialized value in numeric ge (>=) at
/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl line 156, <FILE> line 1 (#2)
......
/usr/local/bioinfo/src/galaxy/galaxy-dist/tools/Nebula/Peak2Bed/peak2bed.pl line 156, <FILE> line 63 (#2)
Use of uninitialized value $fields[1] in conc
**
I dowloaded tool "RepeatMasker" from Galaxy Tool Shed,and RepeatMasker
is installed on our cluster.
Here is the error I get when running the tool RepeatMasker:
An error occurred running this job: /Epilog : job finished at jeu. janv.
31 14:39:16 CET 2013
/work/galaxy/database/pbs/galaxy_4134.sh: line 13: Erreur de syntaxe
près du symbole inattendu « ;; »
/work/galaxy/database/pbs/galaxy_4134.sh: line 13: `RepeatMasker
-parallel 8 -speci/
Do you have any ideas ?
Thank you in advance for your help,
Sarah Maman
--
--*--
Sarah Maman
INRA - LGC - SIGENAE
http://www.sigenae.org/
Chemin de Borde-Rouge - Auzeville - BP 52627
31326 Castanet-Tolosan cedex - FRANCE
Tel: +33(0)5.61.28.57.08
Fax: +33(0)5.61.28.57.53
--*--
9 years, 7 months
Support Question
by Thomas Muench
Hi,
i have installed RepeatExplorer on our local galaxy instance, but with every try, i see only this error message and i don't know why? All installation steps of RepeatExplorer was correctly.
Thank you for your help
Thomas Münch
leibniz-institute for plant genetics and crop plant research
Gatersleben, Germany
Traceback (most recent call last):
File "/opt/galaxy/lib/galaxy/jobs/runners/local.py", line 56, in run_job
job_wrapper.prepare()
File "/opt/galaxy/lib/galaxy/jobs/__init__.py", line 368, in prepare
self.command_line = self.tool.build_command_line( param_dict )
File "/opt/galaxy/lib/galaxy/tools/__init__.py", line 1524, in build_command_line
command_line = fill_template( self.command, context=param_dict )
File "/opt/galaxy/lib/galaxy/util/template.py", line 9, in fill_template
return str( Template( source=template_text, searchList=[context] ) )
File "/opt/galaxy/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__
return getattr(self, mainMethName)()
File "cheetah_DynamicallyCompiledCheetahTemplate_1362033265_04_79640.py", line 92, in respond
NotFound: cannot find '__root_dir__'
failure preparing job
9 years, 7 months
Viral metagenomics
by Mohammad Mohiuddin
Hi,
Can you please tell me how to work with viral metagenomics in Galaxy? When
uploading the data files, there is an option to select the reference genome
but in case of viral metagenomics, I can't select any individual genome.
What will I do in this step? After uploading and processing the data, I will
have to BLAST all my sequences using NCBI BLAST but there is no BLAST option
in galaxy. How can I do that? And, is there any way to change the default
E-value of Galaxy?
Thanks,
Mohiuddin
9 years, 7 months
How to create a tool from a script that loads additional source code files?
by Samuel Lampa
Hi,
I have aGalaxy toolwith some R code which is split up into a few files,
which are loaded by a "master R script", which orcestrates and executes
the whole thing.
I realize that when the master script ("run.R" in my case) is run, it
will not find the other files, since it is itself moved away to a
temporary working directory (something like
".../galaxy/database/job_working_directory/000/165").
Is there any "standard way" of dealing with this, any special toolconfig
syntax etc? ... or do I have to just hard code the absolute paths to the
extra files in my script? :|
Best Regards
// Samuel
--
Developer at SNIC-UPPMAX www.uppmax.uu.se
Developer at Dept of Pharm Biosciences www.farmbio.uu.se
9 years, 7 months
2013 Galaxy Community Conference (GCC2013) Registration and Abstract Submission are Now Open
by Dave Clements
Dear Galaxy Community,
We are pleased to announce that early
registration<http://wiki.galaxyproject.org/Events/GCC2013/Register>
and paper and poster abstract
submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts> are
now open for the 2013 Galaxy Community Conference
(GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013>
. GCC2013 will be held 30 June through July 2 in Oslo Norway, at the
University
of Oslo <http://uio.no/>.
GCC2013 <http://wiki.galaxyproject.org/Events/GCC2013> is an opportunity to
participate in two full days of presentations, discussions, poster
sessions, keynotes, lightning talks and breakouts, all about
high-throughput biology and the tools that support it. The conference also
includes a Training
Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> for
the second year in a row, this year with more in-depth topic coverage, more
concurrent sessions, and more topics.
If you are a biologist or bioinformatician performing or enabling
high-throughput biological research, then please consider attending.
GCC2013 is aimed at:
- Bioinformatics tool developers and data providers
- Workflow developers and power bioinformatics users
- Sequencing and Bioinformatics core staff
- Data archival and analysis reproducibility specialists
*Early registration <http://wiki.galaxyproject.org/Events/GCC2013/Register>*
*saves up to 75% off regular registration costs,* and is very affordable,
with combined registration (Training
Day<http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay> +
main meeting) starting at ~ €95 for post-docs and students. Registering
early also assures you a spot in the Training Day workshops you want to
attend. Once a Training Day session becomes full, it will be closed to new
registrations. Early registration closes 24 May.
*Abstract submission<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts>
* for oral presentations closes 12 April, and for posters on 3 May. Please
consider presenting your work. If you are working with big biological data,
then the people at this meeting want to hear about your work.
Thanks, and hope to see you in Oslo!
The GCC2013 Organizing
Committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers>
PS: And please help get the word
out<http://wiki.galaxyproject.org/Events/GCC2013/Promotion>
!
--
http://galaxyproject.org/GCC2013
<http://galaxyproject.org/wiki/GCC2012>http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://wiki.galaxyproject.org/
9 years, 7 months
