[galaxy-dev] Proposed patch to blastxml_to_tabular.py
Hi there. When trying to convert some BLAST XML to tabular format, from
an old version of BLAST (2.2.15), I had to make some changes to
blastxml_to_tabular.py to get correct results. A patch is enclosed in
this message (and attached). I don't think they should negatively affect
anyone, but the semantics are as follows:
1) If you find an Iteration with no Iteration_query-ID tag, return skip
it, it has no hits.
1) If the Iteration_query-ID tag matches regexp lcl\|\d+_\d+ (e.g.
lcl|1_0) the real accession is in the first word of Iteration_query-def.
2) If the Hit_id matches regexp gnl\|BL_ORD_ID\|d+ (e.g.
gnl|BL_ORD_ID|278) and the Hit_accession tag contains the text of that
\d+ (e.g. 278) then the real accession is in the first word of Hit_def.
I'm basing these semantic on the BLAST reports I've got here, so if
anyone can see an error in them please speak up. Else, here is the patch:
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.pyTue Nov 29
17:35:14 2011 -0500
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.pyWed Nov 30
09:31:11 2011 +0200
@@ -103,7 +103,7 @@
stop_err( "Invalid data format." )
-re_default_query_id = re.compile("^Query_\d+$")
+re_default_query_id = re.compile("^(lcl\|\d+_\d+|Query_\d+)$")
assert re_default_query_id.match("Query_101")
assert not re_default_query_id.match("Query_101a")
assert not re_default_query_id.match("MyQuery_101")
@@ -112,6 +112,7 @@
assert not re_default_subject_id.match("Subject_")
assert not re_default_subject_id.match("Subject_12a")
assert not re_default_subject_id.match("TheSubject_1")
+re_default_subject_id2 = re.compile("^gnl\|BL_ORD_ID\|(\d+)$")
outfile = open(out_file, 'w')
@@ -133,6 +134,9 @@
# 516
# ...
qseqid = elem.findtext("Iteration_query-ID")
+if qseqid == None:
+# no query ID - this happens when there are no hits, so
skip this Iteration
+continue
if re_default_query_id.match(qseqid):
#Place holder ID, take the first word of the query definition
qseqid = elem.findtext("Iteration_query-def").split(None,1)[0]
@@ -152,8 +156,10 @@
#apparently depending on the parse_deflines switch
sseqid = hit.findtext("Hit_id").split(None,1)[0]
hit_def = sseqid + " " + hit.findtext("Hit_def")
-if re_default_subject_id.match(sseqid) \
-and sseqid == hit.findtext("Hit_accession"):
+match2 = re_default_subject_id2.match(sseqid)
+if (re_default_subject_id.match(sseqid) \
+and sseqid == hit.findtext("Hit_accession")) \
+or (match2 and match2.group(1) ==
hit.findtext("Hit_accession")):
#Place holder ID, take the first word of the subject
definition
hit_def = hit.findtext("Hit_def")
sseqid = hit_def.split(None,1)[0]
--- a/tools/ncbi_blast_plus/blastxml_to_tabular.py Tue Nov 29 17:35:14
2011 -0500
+++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py Wed Nov 30 09:31:11
2011 +0200
@@ -103,7 +103,7 @@
stop_err( "Invalid data format." )
-re_default_query_id = re.compile("^Query_\d+$")
+re_default_query_id = re.compile("^(lcl\|\d+_\d+|Query_\d+)$")
assert re_default_query_id.match("Query_101")
assert not re_default_query_id.match("Query_101a")
assert not re_default_query_id.match("MyQuery_101")
@@ -112,6 +112,7 @@
assert not re_default_subject_id.match("Subject_")
assert not re_default_subject_id.match("Subject_12a")
assert not re_default_subject_id.match("TheSubject_1")
+re_default_subject_id2 = re.compile("^gnl\|BL_ORD_ID\|(\d+)$")
outfile = open(out_file, 'w')
@@ -133,6 +134,9 @@
# 516
# ...
qseqid = elem.findtext("Iteration_query-ID")
+if qseqid == None:
+# no query ID - this happens when there are no hits, so skip this
Iteration
+continue
if re_default_query_id.match(qseqid):
#Place holder ID, take the first word of the query definition
qseqid = elem.findtext("Iteration_query-def").split(None,1)[0]
@@ -152,8 +156,10 @@
#apparently depending on the parse_deflines switch
sseqid = hit.findtext("Hit_id").split(None,1)[0]
hit_def = sseqid + " " + hit.findtext("Hit_def")
-if re_default_subject_id.match(sseqid) \
-and sseqid == hit.findtext("Hit_accession"):
+match2 = re_default_subject_id2.match(sseqid)
+if (re_default_subject_id.match(sseqid) \
+and sseqid == hit.findtext("Hit_accession")) \
+or (match2 and match2.group(1) == hit.findtext("Hit_accession")):
#Place holder ID, take the first word of the subject definition
hit_def = hit.findtext("Hit_def")
sseqid = hit_def.split(None,1)[0]
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Re: [galaxy-dev] FASTA manipulation!
Hello David, Renaming with incremental numerical sequence (or with sequence), as you did originally with the tool "NGS: QC and manipulation -> FASTX-Toolkit for FASTQ data -> Rename sequences", is the current option. If your or someone else following Q/A on the list develops a tool that offers a partially fixed/partially incremental numerical renaming operation, it would be nice addition to the Tool Shed. Sorry for the delayed reply. To let you know for next time, the best forum for quick data/tool usage questions would be the galaxy-u...@bx.psu.edu mailing list. http://galaxyproject.org/wiki/Support#Public_mailing_list_Q_.26_A_discussions http://galaxyproject.org/wiki/Mailing%20Lists Best wishes for your project, Jen Galaxy team On 9/23/11 10:05 AM, David PANG wrote: Dear All, I am new to Galaxy! When I tried to manipulate mt fasta sequences from RNA-Seq, I just add >1, >2...>100 etc! Right now, I am trying to add libraryA to all of the sequences like >libraryA_1, >libraryA_2.>libraryA_100. I can not figure out how to do it on Galaxy. Could somebody help to this end. Thanks David -- David PANG, Ph.D. ___ 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://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
Re: [galaxy-dev] proxy settings?
Found the cure - just required adding urllib2.ProxyHandler in the data_source
tools.
Why doesn't Galaxy pick up the system http_proxy variables?
--Russell Smithies
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Smithies, Russell
Sent: Wednesday, 30 November 2011 9:09 a.m.
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] proxy settings?
I'm new to Galaxy so I'm not sure if this a Galaxy or linux/apache question .
When I try to "Get Data" from UCSC or any other external site, I get a 407
error from our proxy as I need to authenticate.
Is the request going out as the 'galaxy' user or 'apache' or the user that's
logged in?
I already have http_proxy and ftp_proxy configured in /etc/profile (we're
running Centos 6) but I assume there a correct place to configure this for
Galaxy?
The error message I'm seeing is:
An error occurred running this job: The remote data source application may be
off line, please try again later. Error: ('http error', 407, 'Proxy Access
Denied', )
Any ideas?
Thanx,
Russell Smithies
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Re: [galaxy-dev] Job output not returned from cluster
On Nov 29, 2011, at 3:13 AM, Peter Cock wrote: > On Monday, November 28, 2011, Joseph Hargitai > wrote: > > Ed, > > > > we had the classic goof on our cluster with this. 4 nodes could not see the > > /home/galaxy folder due to a missing entry in /etc/fstab. When the jobs hit > > those nodes (which explains the randomness) we got the error message. > > > > Bothersome was the lack of good logs to go on. The error message was too > > generic - however I discovered that Galaxy was depositing the error and our > > messages in the /pbs folder and you could briefly read them before they got > > deleted. There the message was the classic SGE input/output message - > > /home/galaxy file not found. > > > > Hence my follow up question - how can I have galaxy NOT to delete these SGE > > error and out files? > > > > best, > > joe > > Better yet, Galaxy should read the SGE o and e files and record their > contents as it would for a directly executed tools stdout and stderr. > > Peter ...or at least have the option to do so, maybe a level of verbosity. I have been bitten by lack of stderr output myself, where having it might have saved some manual debugging. chris ___ 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/
Re: [galaxy-dev] custom indexes
Hello Candace, Hopefully you have already discovered this, but genomes can be loaded (usually using FTP) into a history and used as a custom genome with many tools. The genomes are loaded in fasta format and indexes are generated by the tools themselves. Most tools that use a reference genome include an option to use a custom reference genome (including Tophat and the other Tuxedo tools). Sorry for the delay in reply. Next time, for a data or tool use question, the galaxy-u...@bx.psu.edu mailing list would probably be a better choice (lower volume and reserved for usage topics). http://galaxyproject.org/wiki/Support#Public_mailing_list_Q_.26_A_discussions http://galaxyproject.org/wiki/Mailing%20Lists Best wishes for your project, Jen Galaxy team On 9/22/11 7:00 AM, Candace Seeve wrote: I'd like to map RNA-Seq data from two different bacterial species to their genomes. How do I go about getting a custom index added to the galaxy server? One of the genomes is not yet published so is it possible to keep the indexes private? Thanks, Candace ___ 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://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
Re: [galaxy-dev] Integration with LIMS
Hello Bernhard, I came across your question and see that you may never have had a reply. If you have this already worked out, then great! But if not, perhaps the API wikis will be of interest: http://galaxyproject.org/wiki/Learn/API The documentation is still in progress, but the main points are present and the examples should be helpful. The general idea is that the LIMS system should be able to communicate with Galaxy via the API. If you have specific question about any unresolved issues around LIMS/API integration, please send a brand new question (new email, new thread, new subject) to the galaxy-dev mailing list and we will do our best to offer (quicker!) help. Our sincere apologies for the delayed reply, Best, Jen Galaxy team On 6/22/11 3:51 AM, Sonderegger Bernhard wrote: Hello, I am exploring the possibility of using a local galaxy installation for light bioinformatics on sequence data in the scope of an existing LIMS system. Ideally I would like to be able to do the following 1. Push datasets from the LIMS to galaxy (directly into the user's account or into a fresh temporary session) 2. Allow the user to perform tasks within galaxy, backtracking and retrying as necessary. 3. Push the results along with the galaxy history (ideally converted to a workflow) back to the LIMS 4. (Allow workflows stored in the LIMS to be pushed to Galaxy along with further datasets or even completely automatic launch of these workflows from within the LIMS) Is this feasible? How much wrok would be required? Since I am new to Galaxy (at least from the development side), I would very much appreciate comments advice and pointers to documentation or existing projects of a similar nature. Thanks in advance, Bernhard ___ 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://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
Re: [galaxy-dev] trannsfer files from remote system to galaxy
Hello, In case you have not found the answers in the wiki yet, a link to the administration details for data libraries are: General/All: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries Loading Data: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files Hopefully this is already resolved or this helps! Take care, Jen Galaxy team On 9/8/11 6:05 AM, shashi shekhar wrote: Hi, In my local instance of Galaxy ,I want to add one option in which i can get files from remote system to galaxy in data library . except url is there any option to get remote files from galaxy ? Regards ___ 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://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
Re: [galaxy-dev] tophat xml that supports SOLID colorspace
Hello, Perhaps you have found this in the source already, but if not, a version of the Tophat tool for SOLiD is available. It is on the test server only, should be used with caution, and is completely unsupported. In the Galaxy source at bitbucket, please see: tophat_color_wrapper.xml at https://bitbucket.org/galaxy/galaxy-central/src/b751663f3f64/tools/ngs_rna On the Galaxy test server under "NGS: RNA Analysis -> Tophat for SOLiD" http://test.g2.bx.psu.edu/ Hopefully this helps! Best, Jen Galaxy team On 9/6/11 12:47 AM, KOH Jia Yu Jayce wrote: Hi, I am looking for tophat xml that supports SOLID colorspace. Is it anywhere available? Thanks a lot. ___ 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://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
Re: [galaxy-dev] galaxy core services vs wrapper.py duplication & caching of .fai files
Curtis, > [curtish@cheaha galaxy]$ find . -name "*.py" | xargs grep sam_fa_indices.loc > ./tools/samtools/sam_pileup.py:seqFile = '%s/sam_fa_indices.loc' % > GALAXY_DATA_INDEX_DIR ... > ./tools/ngs_rna/cufflinks_wrapper_without_gtf.py: > cached_seqs_pointer_file = os.path.join( options.index_dir, > 'sam_fa_indices.loc' ) > > Is there any place in galaxy-core where such a core service lives and could > be used by all these adaptors, rather than replicating the code everywhere? Not yet, but this is definitely needed. However, tools and Galaxy must remain independent , so the location of needed indices should be passed to the tool via the command line rather than having tools call into Galaxy. > As a related question, for fasta genomes from the current history, these > wrappers compute the .fai file on the fly, in TMP, then throw it away, every > time. Has there been any discussion about storing such derived indices in the > dataset’s metadata (like the .bai file on a .bam data set), so it gets > computed once, then re-used? Converted datasets, which subsume indices-as-metadata, can store dataset indices. Extending converted datasets to store indices created on the fly is also very much needed. Any community contributions that address these issues would be most welcome. Best, J.___ 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/
[galaxy-dev] proxy settings?
I'm new to Galaxy so I'm not sure if this a Galaxy or linux/apache question .
When I try to "Get Data" from UCSC or any other external site, I get a 407
error from our proxy as I need to authenticate.
Is the request going out as the 'galaxy' user or 'apache' or the user that's
logged in?
I already have http_proxy and ftp_proxy configured in /etc/profile (we're
running Centos 6) but I assume there a correct place to configure this for
Galaxy?
The error message I'm seeing is:
An error occurred running this job: The remote data source application may be
off line, please try again later. Error: ('http error', 407, 'Proxy Access
Denied', )
Any ideas?
Thanx,
Russell Smithies
===
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from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
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[galaxy-dev] GATK / R local install configuration
Hi, I'm testing the GATK pipeline and I ran into a problem with "Variant Recalibrator" tool. It seems I don't have correctly configure R and GATK on my instance, as this tool is failing with this error: mv: /Volumes/Data/Users/cjavier/galaxy_central/database/files/000/dataset_393.dat.pdf: No such file or directory I see this PDF is builded with R and I also see this in the log file: INFO 17:11:44,260 VariantRecalibrator - Executing: Rscript /Volumes/Data/Users/cjavier/galaxy_central/database/files/000/dataset_393.dat WARN 17:11:48,407 RScriptExecutor - RScript exited with 1. Run with -l DEBUG for more info. In the testing server this tool does work: http://test.g2.bx.psu.edu/u/cjav/h/variant-recalibrator---tutorial At least after making sure the input VCF file has matching annotations string to the one you want to select in Galaxy. Any help on what need to be done to get this configuration right. BTW I already have R and Rpy correctly configured and I can run tools like "Statistics/Summary Statistics". Thanks! Carlos ___ 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/
[galaxy-dev] galaxy core services vs wrapper.py duplication & caching of .fai files
Folks, I was writing a samtools/mpileup wrapper for our local use. When I delved into how the existing samtools/sam_pileup.py adaptor worked, if found that it has a local copy of the routine to look up the samtools .fai file in sam_fa_indices.loc for "installed" genomes. I then noticed that this routine is duplicated in many different adaptors: [curtish@cheaha galaxy]$ find . -name "*.py" | xargs grep sam_fa_indices.loc ./tools/samtools/sam_pileup.py:seqFile = '%s/sam_fa_indices.loc' % GALAXY_DATA_INDEX_DIR ./tools/samtools/sam_mpileup_view.py:seqFile = '%s/sam_fa_indices.loc' % GALAXY_DATA_INDEX_DIR ./tools/samtools/sam_to_bam.py:cached_seqs_pointer_file = '%s/sam_fa_indices.loc' % options.index_dir ./tools/ngs_rna/cufflinks_wrapper_with_gtf.py:cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) ./tools/ngs_rna/cuffdiff_wrapper.py:cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) ./tools/ngs_rna/cufflinks_wrapper.py:cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) ./tools/ngs_rna/cuffcompare_wrapper.py:cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) ./tools/ngs_rna/cufflinks_wrapper_without_gtf.py: cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) Is there any place in galaxy-core where such a core service lives and could be used by all these adaptors, rather than replicating the code everywhere? As a related question, for fasta genomes from the current history, these wrappers compute the .fai file on the fly, in TMP, then throw it away, every time. Has there been any discussion about storing such derived indices in the dataset's metadata (like the .bai file on a .bam data set), so it gets computed once, then re-used? ___ 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/
Re: [galaxy-dev] downloading bowtie indexed files
Hi Nik, Native and custom reference genome indexes cannot be downloaded from Galaxy. However, the Galaxy team knows that this is high interest and a few delivery options are under consideration. Apologies for the delay in reply, Best, Jen Galaxy team On 9/2/11 3:26 PM, Nikhil Joshi wrote: Hi all, Just wondering if there is a way to download the bowtie indexed files after indexing. It seems that the indexed output is simply a meta-file that points to the directory where the indexed files are kept but what if I want to download all of the indexed files themselves? I wrote something to do this... basically I created an html page that is the output of bowtie-build which then points to the created files... but I'm wondering if there is an easier way...? - Nik. ___ 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://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
Re: [galaxy-dev] Can not clean my galaxy datasets
Hello Liram, Perhaps the allow_user_dataset_purge option has not been set to True in universe_wsgi.ini? Please see this wiki for details: http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas#Quotas Hopefully this helps, but please let us know if you need more assistance, Best, Jen Galaxy team On 11/29/11 5:44 AM, liram_va...@agilent.com wrote: Hello, My name is Liram Vardi and I’m using local Galaxy instance. Anyway, I can’t clean my deleted datasets from my own locally disk. When I am trying to delete dataset, as was explained in http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions, First, I used the “delete 'X' icon" near the dataset to delete the dataset, Then, when I go to "Options -> Show Deleted Datasets", I can see my “deleted dataset” on the list with the note: /"This dataset has been deleted. Click _here_ to undelete it”//*but I don’t get the also the option “or _here_ to immediately remove it from disk."*/. Also, when I use the option “Options -> Purge Deleted Datasets”, I’m getting a message “0 datasets have been deleted permanently” and my deleted dataset still stays in the "Options -> Show Deleted Datasets" menu list. I also tried to clear the history, but when I’m doing that, the “using X Mb” tab on the upper right corner is still not reset. What is the problem? Thanks a lot for your help! Liram ___ 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://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
[galaxy-dev] Can not clean my galaxy datasets
Hello, My name is Liram Vardi and I'm using local Galaxy instance. Anyway, I can't clean my deleted datasets from my own locally disk. When I am trying to delete dataset, as was explained in http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Actions, First, I used the "delete 'X' icon" near the dataset to delete the dataset, Then, when I go to "Options -> Show Deleted Datasets", I can see my "deleted dataset" on the list with the note: "This dataset has been deleted. Click _here_ to undelete it" but I don't get the also the option "or _here_ to immediately remove it from disk." . Also, when I use the option "Options -> Purge Deleted Datasets", I'm getting a message "0 datasets have been deleted permanently" and my deleted dataset still stays in the "Options -> Show Deleted Datasets" menu list. I also tried to clear the history, but when I'm doing that, the "using X Mb" tab on the upper right corner is still not reset. What is the problem? Thanks a lot for your help! Liram ___ 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/
Re: [galaxy-dev] Question about from_work_dir
>> Aurelien, >> >> The particular behavior that you need isn't currently supported because the >> value of from_work_dir isn't treated as a template. To work around this >> limitation, you can do the move/copy operations in your tool wrapper; see >> the wrappers for Bowtie and Sicer for examples on how to do this. >> >> Good luck, >> J. > > Hi Jeremy, > > Is it possible to build the required string elsewhere in the .xml file using > cheetah and then pass the resulting string like from_work_dir=$result or is > using a wrapper really the only way to go? I'm writing a config for a tool > that names the output files using the options, so I could potentially > concatenate the option values to get the required file name if I could do > that. Alex, The best approach is for your tool to accept output file names; then, in the command_line tag of the tool wrapper XML, you can build the output name based on options chosen by the user. Finally, please always cc the mailing list for community and archival purposes. Thanks, J. ___ 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/
Re: [galaxy-dev] Job output not returned from cluster
On Monday, November 28, 2011, Joseph Hargitai < joseph.hargi...@einstein.yu.edu> wrote: > Ed, > > we had the classic goof on our cluster with this. 4 nodes could not see the /home/galaxy folder due to a missing entry in /etc/fstab. When the jobs hit those nodes (which explains the randomness) we got the error message. > > Bothersome was the lack of good logs to go on. The error message was too generic - however I discovered that Galaxy was depositing the error and our messages in the /pbs folder and you could briefly read them before they got deleted. There the message was the classic SGE input/output message - /home/galaxy file not found. > > Hence my follow up question - how can I have galaxy NOT to delete these SGE error and out files? > > best, > joe Better yet, Galaxy should read the SGE o and e files and record their contents as it would for a directly executed tools stdout and stderr. Peter ___ 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/
