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What script updates the umask of database/files/* and deletes database/job_working_directory
by Chorny, Ilya 27 Aug '11

27 Aug '11

When running as the actual user in drama, I made it so the .dat files are not initially created so that when a tool moves data from the a temp directory to the out .dat file it will not fail. (i.e. unix does not allow moving a file owned by one user to a file owned by another user because mv carries the attributes of the original file). Now I want to change the ownership of the files through a sudo call at the end. Which script is run at the end to clean things up? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny(a)illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>

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Re: [galaxy-dev] [galaxy-user] Cuffdiff question about using an unspecified (?) database/build
by Jennifer Jackson 26 Aug '11

26 Aug '11

Hi Curtis, This is a good question. I'll post back to the list to (hopefully) gather some feedback. Thanks! Jen On 8/25/11 8:44 AM, Robert Curtis Hendrickson wrote: > Wonderful. We're on galaxy-dist, but we can pull that patch. > Are most local installs on Dist or Central? > > Thanks! > > Curtis > > > >> -----Original Message----- >> From: Jennifer Jackson [mailto:jen@bx.psu.edu] >> Sent: Thursday, August 25, 2011 10:41 AM >> To: Robert Curtis Hendrickson >> Cc: David K Crossman; 'galaxy-dev(a)lists.bx.psu.edu' >> Subject: Re: [galaxy-user] Cuffdiff question about using an unspecified (?) >> database/build >> >> Hi Curtis, >> >> Changeset details: >> http://bitbucket.org/galaxy/galaxy-central/changeset/07de40a5a0b9 >> >> We are planning on releasing a distribution within a week, so >> alternatively you could wait and pull from there, if you normally work >> from the galaxy-dist repository. >> >> And for everyone tracking this fix: the changeset was applied to the >> public Galaxy main instance yesterday (http://usegalaxy.org) >> >> Hope this helps! >> >> Jen >> Galaxy team >> >> On 8/25/11 7:55 AM, Robert Curtis Hendrickson wrote: >>> Jen, >>> >>> Can you also please describe the details of the fix? >>> We need to fix the same issue in our local instance, but don't know if this >> was a fix to cuffdiff, or to galaxy. Which one should we be updating? >>> >>> Regards, >>> Curtis -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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tool which using web service
by shashi shekhar 26 Aug '11

26 Aug '11

hi, I have application , i want to integrate that application like ucsc_browser in my local instance of galaxy .Application create some input data ,that data i want to send into galaxy to process. can u help me how can i add such type of tool in Galaxy ? Regards shashi

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can someone explain outputs of bowtie_wrapper.xml?
by Nikhil Joshi 26 Aug '11

26 Aug '11

Hi all, I am trying to figure out the meaning of the XML within the <outputs>...</outputs> portion of the bowtie_wrapper.xml file. The tool config syntax page doesn't really explain the details that well. Can someone point me to somewhere, or just explain, what is going on? For example, here is the outputs part of that file: <outputs> <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> <actions> <conditional name="refGenomeSource.genomeSource"> <when value="indexed"> <action type="metadata" name="dbkey"> <option type="from_data_table" name="bowtie_indexes" column="1" offset="0"> <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> <filter type="param_value" ref="refGenomeSource.index" column="0"/> </option> </action> </when> <when value="history"> <action type="metadata" name="dbkey"> <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> </action> </when> </conditional> </actions> </data> <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)"> <filter>(( singlePaired['sPaired'] == "single" and singlePaired['sParams']['sSettingsType'] == "full" and singlePaired['sParams']['sMaxFile'] is True ) or ( singlePaired['sPaired'] == "paired" and singlePaired['pParams']['pSettingsType'] == "full" and singlePaired['pParams']['pMaxFile'] is True )) </filter> <actions> <conditional name="singlePaired.sPaired"> <when value="single"> <action type="format"> <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> </action> </when> <when value="paired"> <action type="format"> <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> </action> </when> </conditional> </actions> </data> <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)"> <filter>singlePaired['sPaired'] == "paired"</filter> <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter> <filter>singlePaired['pParams']['pMaxFile'] is True</filter> <actions> <conditional name="singlePaired.sPaired"> <when value="single"> <action type="format"> <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> </action> </when> <when value="paired"> <action type="format"> <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> </action> </when> </conditional> </actions> </data> <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)"> <filter> (( singlePaired['sPaired'] == "single" and singlePaired['sParams']['sSettingsType'] == "full" and singlePaired['sParams']['sUnmappedFile'] is True ) or ( singlePaired['sPaired'] == "paired" and singlePaired['pParams']['pSettingsType'] == "full" and singlePaired['pParams']['pUnmappedFile'] is True )) </filter> <actions> <conditional name="singlePaired.sPaired"> <when value="single"> <action type="format"> <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> </action> </when> <when value="paired"> <action type="format"> <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> </action> </when> </conditional> </actions> </data> <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)"> <filter>singlePaired['sPaired'] == "paired"</filter> <filter>singlePaired['pParams']['pSettingsType'] == "full"</filter> <filter>singlePaired['pParams']['pUnmappedFile'] is True</filter> <actions> <conditional name="singlePaired.sPaired"> <when value="single"> <action type="format"> <option type="from_param" name="singlePaired.sInput1" param_attribute="ext" /> </action> </when> <when value="paired"> <action type="format"> <option type="from_param" name="singlePaired.pInput1" param_attribute="ext" /> </action> </when> </conditional> </actions> </data> </outputs> It seems like each output has conditionals, some of which are setting DB keys, but with others I can't tell what is going on. For example, I can't find anything about a "type" or "name" or "param_attribute" value that you can set within the <option> tag, for example. Anybody know what those mean? Also, still can't really figure out what values are possible to set for the <action> tag. Any help would highly appreciated. Thanks! - Nik.

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Updated Cufflinks Wrapper
by Chorny, Ilya 26 Aug '11

26 Aug '11

I made some changes to the cufflinks wrapper. I added the -g/--GTF-guide use reference transcript annotation to guide assembly as an option. The version number needs to still be updated in my commit. https://bitbucket.org/ichorny/galaxy-central/changeset/fc5e24d453e5 Ilya Chorny Ph.D. Bioinformatics - Intern ichorny(a)illumina.com<mailto:ichorny@illumina.com> 858-202-4582

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"filtering" BED files by score in trackster
by Hans-Rudolf Hotz 26 Aug '11

26 Aug '11

Hi The option to filter a BED file by the score in the visualization tool is brilliant! There is just one draw back: you can only filter by integers. Hence a score of 1.1 is the same as of score of 1.3. How difficult would it be to change the code in order to allow floats for the filter? Such a feature would help us a lot! I tried to dig into the visualization code...but I got lost. Thank you very much for your help Regards, Hans

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Re: [galaxy-dev] [galaxy-user] Cuffdiff question about using an unspecified (?) database/build
by Robert Curtis Hendrickson 26 Aug '11

26 Aug '11

Jen, Can you also please describe the details of the fix? We need to fix the same issue in our local instance, but don't know if this was a fix to cuffdiff, or to galaxy. Which one should we be updating? Regards, Curtis > -----Original Message----- > From: galaxy-user-bounces(a)lists.bx.psu.edu [mailto:galaxy-user- > bounces(a)lists.bx.psu.edu] On Behalf Of David K Crossman > Sent: Friday, August 19, 2011 11:10 AM > To: Jennifer Jackson > Cc: galaxy-user (galaxy-user(a)lists.bx.psu.edu) > Subject: Re: [galaxy-user] Cuffdiff question about using an unspecified (?) > database/build > > Jen, > > Thank you very much for the reply. I'm glad to know it is a known bug > and not something on my side of things. So, would my analysis be affected if > I did change the bam file "Database/Build" to the older tree shrew version > found in the drop down list? What significance does this "Database/Build" box > have in downstream analysis if you have your own fasta reference genome file > and gtf annotation file that is being referenced instead of a locally cached > one? I'm just trying to obtain a better understanding of the "Database/Build" > box for analyses where I provide the fasta and gtf file. > > Thanks, > David > > > -----Original Message----- > From: Jennifer Jackson [mailto:jen@bx.psu.edu] > Sent: Friday, August 19, 2011 9:20 AM > To: David K Crossman > Cc: galaxy-user (galaxy-user(a)lists.bx.psu.edu) > Subject: Re: [galaxy-user] Cuffdiff question about using an unspecified (?) > database/build > > Hello David, > > This is a known bug. The correction is planned to be moved out onto the public > Galaxy instance at the next update (within a week). > > Sorry for the current inconvenience, > > Best, > > Jen > Galaxy team > > On 8/19/11 7:00 AM, David K Crossman wrote: > > Hello! > > > > I have an RNA-Seq project which consists of 5 samples from the species > > tree shrew. When uploading these fastq files into Galaxy, I chose > > "unspecified (?)" for the database/build since the latest tree shrew > > version is not in the drop down list. When using TopHat, > > Cufflinks/Compare I have selected a reference genome from my history > > instead of using a built-in index, as well as a gtf annotation file > > for Cufflinks/Compare and everything has been working fine. Now, I am > > at the Cuffdiff step and I am running into an error when setting it up > > to perform replicate analysis. When I select my TopHat accepted hits > > bam file I see a red X and the error: "Unspecified genome build, click > > the pencil icon in the history item to set the genome build." Here's a > > screenshot of what I'm seeing: > > > > Since the latest reference genome for tree shrew wasn't listed, that's > > why I chose "unspecified (?)." Should I go back and edit these > > accepted hits bam files to say the Database/Build from the drop down > > list is "Tree shrew Dec. 2006 (Broad/tupBel1) (tupBel1)?" I know that > > this is simple to change, but will this affect my results in any way? > > Any help/info would be greatly appreciated. > > > > Thanks, > > > > David > > > > > > > > ___________________________________________________________ > > 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://usegalaxy.org > http://galaxyproject.org/Support > > ___________________________________________________________ > 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/

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Galaxy public instances: data and job quotas
by Jennifer Jackson 25 Aug '11

25 Aug '11

Galaxy public instances: data and job quotas User data and job quota limits are now implemented at the public Galaxy Test instance http://test.g2.bx.psu.edu: http://galaxyproject.org/Test#Quotas While no quotas are currently implemented at the public Galaxy Main instance http://usegalaxy.org, we do ask that users stay within certain usage limits: http://galaxyproject.org/Main#Quotas If you find that you require additional resources, please consider the alternative Galaxy options explained at: http://galaxyproject.org/Big%20Picture/Choices Thanks for using Galaxy!

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Error when using build_profile_indexes.py on hg19
by Sarah Diehl 25 Aug '11

25 Aug '11

Hi everybody, when I run the build_profile_indexes.py script in the scripts/tools/annotation_profiler/ directory on hg19 (downloaded yesterday from UCSC), I get the following error: Created table dir (profiled_annotations/hg19/wgEncodeOpenChromFaireGlioblaBaseOverlapSignal). ['fileName'] Table wgEncodeOpenChromFaireGlioblaBaseOverlapSignal (/galaxy/galaxy_data/ucsc_data/hg19/wgEncodeOpenChromFaireGlioblaBaseOverlapSignal.sql) does not appear to have a chromosome, a start, or a stop. Removing empty table (wgEncodeOpenChromFaireGlioblaBaseOverlapSignal) directory (profiled_annotations/hg19/wgEncodeOpenChromFaireGlioblaBaseOverlapSignal). Created table dir (profiled_annotations/hg19/wgEncodeCshlShortRnaSeqK562ChromatinShortTransfrags). ['bin', 'chrom', 'chromStart', 'chromEnd', 'name', 'score', 'strand', 'length', 'numUnique', 'numReads', 'minSeqCount', 'maxSeqCount', 'aveSeqCount', 'firstSeqCount', 'medSeqCount', 'thirdSeqCount', 'minReadCount', 'maxReadCount', 'aveReadCount', 'firstReadCount', 'medReadCount', 'thirdReadCount', 'numRegions', 'regStart', 'regLength', 'seqCount', 'regCount', 'sumCount', 'KEY', 'KEY'] Traceback (most recent call last): File "/galaxy/galaxy_backup/galaxy-dist/scripts/tools/annotation_profiler/build_profile_indexes.py", line 338, in <module> if __name__ == "__main__": __main__() File "/galaxy/galaxy_backup/galaxy-dist/scripts/tools/annotation_profiler/build_profile_indexes.py", line 310, in __main__ bitset_dict[ chrom ].set_range( start, end - start ) File "bitset.pyx", line 128, in bx.bitset.BitSet.set_range (lib/bx/bitset.c:1130) File "bitset.pyx", line 93, in bx.bitset.b_check_range_count (lib/bx/bitset.c:656) IndexError: End 16573 is larger than the size of this BitSet (16571). Everything worked fine with mm9 and dm3. Since the script wasn't changed in the last year, I suspect it has to do with the UCSC data. We don't really use hg19, so I'm fine with just leaving it out for now, but I wanted to report the error anyway. Best regards, Sarah

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creating new input/output formats
by Nikhil Joshi 25 Aug '11

25 Aug '11

Hi all, Is there a relatively easy way to create your own input/output formats? Some of the formats from programs that I am trying to install on our local Galaxy do not exist as an option. Any ideas? - Nik.

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