[galaxy-user] Searching Galaxy Tool Shed gives error
Hello, Searching the Galaxy toolshed for workflows on http://toolshed.g2.bx.psu.edu/ gives an error Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Cheers Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Searching Galaxy Tool Shed gives error
Hello Joachim, Thanks for reporting this. This issue was resolved a couple of weeks ago, but did not make it into the cutoff for the last Galaxy distribution release. It is corrected on the test Galaxy tool shed and will be included in the next Galaxy release. Greg Von Kuster On Dec 12, 2012, at 4:52 AM, Joachim Jacob wrote: Hello, Searching the Galaxy toolshed for workflows on http://toolshed.g2.bx.psu.edu/ gives an error Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Cheers Joachim -- Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] How to add to add hg16 index into the build-in index / reference gnome list?
How do I add hg16 into the build-in index? ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] [galaxy-dev] How to add to add hg16 index into the build-in index / reference gnome list?
Hello Sachit, Instructions for setting up local indexes are in our wiki here: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Bowtie2 is not specifically listed, but the instructions for Bowtie and Bowtie2 are nearly identical. The same indexes are used for Bowtie2 and Tophat2. When building the index, you simply replace bowtie-build with bowtie2-build in the command string and create/modify the bowtie2_index.loc file the same as you would the bowtie_index.loc file. The Tophat2 manual has some more details about getting set up here: http://tophat.cbcb.umd.edu/manual.html Next time, for questions about local installs, using just the galaxy-...@bx.psu.edu list is best (no need to post to multiple lists). If your question has been misunderstood, please send more details to clarify. Best, Jen Galaxy team On 12/12/12 3:46 AM, Sachit Adhikari wrote: How do I add hg16 into the build-in index? ___ 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/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] GATK Not running
Hi Umar,
Can you click the eye icon to view the contents of the 'log' dataset for the
GATK run. The end of the log should have the actual error encountered (the text
you provided is a bit of a red herring)
Since you are using hg19, the most likely cause for the error is that the
reference fasta file you are using is not ordered properly, or that your
alignments were made using a different genome (e.g. alignment with bwa using
built-in hg19 [not ordered properly] and then GATK using a different hg19 fasta
from your history.)
If you are using a custom genome, make sure that it is GATK-ordered and that
the same one is used in all steps; there is an hg19 GATK-ordered fasta file
available in a Data library ('GATK') on Main.
Thanks for using Galaxy,
Dan
On Dec 11, 2012, at 12:11 PM, Farooq,Umar (res) wrote:
Hi,
I am trying to incorporate GATK in my pipeline but not been able to make it
work. I aligned my data with Hg 19 and then ran sam tool filter and then
picard duplicate removal. I uploaded dbSNP and the reference FASTA file for
Hg 19 in galaxy to run this pipeline. But for some reason GATK tool for base
recalibration will not accept this output file. I wonder if there is sorting
or indexing issue but how to fix this in galaxy.
An error occurred running this job: Picked up _JAVA_OPTIONS:
-Djava.io.tmpdir=/space/g2main [Mon Dec 10 10:30:42 EST 2012]
net.sf.picard.sam.CreateSequenceDictionary
REFERENCE=/space/g2main/tmp-gatk-tKp41A/gatk_input.fasta
OUTPUT=/space/g2main/tmp-gatk-tKp41A/dict3503196447953523717.tmp
Thanks,
Umar
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___
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Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using reply all in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
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Re: [galaxy-user] GATK Not running
Hi Philippe, The GATK wrappers provided with the Galaxy distribution are for GATK version 1.4. There is a set of 1.6/GATK-lite wrappers that has been developed by the team, but is not yet available. There may also be other options available in the Tool Shed that have been contributed by the community. Thanks for using Galaxy, Dan On Dec 11, 2012, at 5:26 PM, Philipe Moncuquet wrote: Hi, I have encountered the same kind of errors. When I update the loc files link to GATK, some of the tools display the reference genomes I added and some not. It seems that the galaxy wrapper for GATK 1.6 is not very functional. GATK don't really care because they are not supporting it any more, even documentation has disappeared. And I understand that galaxy developers have other stuff to do than supporting a tool that will disappear because it's not open source any more. I don't know what tool could replace the recalibration process done by GATK and don't know how to correct bugs neither. Any suggestions ? Philippe 2012/12/12 Farooq,Umar (res) ufar...@resident.uchc.edu Hi, I am trying to incorporate GATK in my pipeline but not been able to make it work. I aligned my data with Hg 19 and then ran sam tool filter and then picard duplicate removal. I uploaded dbSNP and the reference FASTA file for Hg 19 in galaxy to run this pipeline. But for some reason GATK tool for base recalibration will not accept this output file. I wonder if there is sorting or indexing issue but how to fix this in galaxy. An error occurred running this job: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/space/g2main [Mon Dec 10 10:30:42 EST 2012] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/space/g2main/tmp-gatk-tKp41A/gatk_input.fasta OUTPUT=/space/g2main/tmp-gatk-tKp41A/dict3503196447953523717.tmp Thanks, Umar ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] GATK Not running
Hi Joshua, Is this on the main public site? If so, can you share your history with me and I'll take a look? If this is on a local instance, can you provide additional information, such as the GATK version that you are using? Thanks for using Galaxy, Dan On Dec 11, 2012, at 5:34 PM, Joshua Orvis wrote: I'm having some problems with GATK as well, but do have a functional pipeline that uses the following GATK tools in Galaxy: - Realigner Target Creator - Indel Realigner - Unified Genotyper - Variant Filtration The main problem I'm having with them is that it seems I need to run the fasta/fastq groomer on all inputs before starting, and if I attempt to use the 'advanced' options on either of the last two steps above it fails immediately every time with a command-line option parsing error. I plan on digging into the wrapper script in the coming days in an attempt to correct this, which is currently attributed to Dan Blankenberg. I'm relatively new to Galaxy development though and don't know where to submit my updates though should I fix any of these problems. Joshua On Tue, Dec 11, 2012 at 4:26 PM, Philipe Moncuquet philippe.m...@gmail.com wrote: Hi, I have encountered the same kind of errors. When I update the loc files link to GATK, some of the tools display the reference genomes I added and some not. It seems that the galaxy wrapper for GATK 1.6 is not very functional. GATK don't really care because they are not supporting it any more, even documentation has disappeared. And I understand that galaxy developers have other stuff to do than supporting a tool that will disappear because it's not open source any more. I don't know what tool could replace the recalibration process done by GATK and don't know how to correct bugs neither. Any suggestions ? Philippe 2012/12/12 Farooq,Umar (res) ufar...@resident.uchc.edu Hi, I am trying to incorporate GATK in my pipeline but not been able to make it work. I aligned my data with Hg 19 and then ran sam tool filter and then picard duplicate removal. I uploaded dbSNP and the reference FASTA file for Hg 19 in galaxy to run this pipeline. But for some reason GATK tool for base recalibration will not accept this output file. I wonder if there is sorting or indexing issue but how to fix this in galaxy. An error occurred running this job: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/space/g2main [Mon Dec 10 10:30:42 EST 2012] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/space/g2main/tmp-gatk-tKp41A/gatk_input.fasta OUTPUT=/space/g2main/tmp-gatk-tKp41A/dict3503196447953523717.tmp Thanks, Umar ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Link to display BED files in UCSC Genome Browser
Hi Luce, We can duplicate the missing link problem and are in the processing of investigating/correcting. Thank you for reporting the issue! Jen Galaxy team On 12/11/12 5:36 AM, Lucy A. Skrabanek wrote: Dear all, For BED files, there used to be an option in the preview window to visualize them in the UCSC Genome Browser, but that seems to have disappeared. Specifically, from a TopHat/Cufflinks run, I used to be able to visualize the accepted hits, the splice junctions and the assembled transcripts datasets in the UCSC Genome browser by simply clicking on the 'display at UCSC' link. This link is still available for the accepted hits dataset, but seems to have disappeared for the other two datasets. I realize I can still visualize these datasets by downloading them (although this seems somewhat less convenient). Is the loss of this link to UCSC intentional? Thanks, luce ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Should fastq files be merged?
Hello Karen, It sounds as if the data contains replicates, but this should be confirmed with the data source by reviewing the methods for the specific experiment. If indeed these are replicates, it is best to process these independently and submit them as replicates when using the NGS: RNA-seq tools. The tool authors have specific advice regarding replicates at their web site: http://cufflinks.cbcb.umd.edu/howitworks.html#reps If just different conditions, you would also want to process independently - this is probably obvious but I wanted to mention it just to be complete. Links to resources, including a Galaxy tutorial, can be found grouped in our wiki at: http://wiki.galaxyproject.org/Support#Tools_on_the_Main_server Hopefully this helps, Jen Galaxy team On 12/11/12 11:03 AM, Karen Margrethe Jessen wrote: Hi, I have downloaded the fastq.tgz files for an ENCODE RNA-SEQ data and unpacked the files. The data set is paired end illumina. I am a bit confused, as there are 5 files for read1 and 5 files for read2 for each sample. Am I supposed to merge the 5 files before aligning to the hg19 genome? If yes, how should I merge these files? I would greatly appreciate any help you can provide. Best regards, Karen Margrethe Jessen Cand. Scient., ph.d.-student Aarhus University Denmark ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
