galaxy-dev August 2013

galaxy-dev@lists.galaxyproject.org

116 participants
210 discussions

Blast+: new feature filter/mask... by taxid before job in one task
by Berner, Thomas 26 Feb '14

26 Feb '14

Hi guys, We recently installed NCBI BLAST + to our local Galaxy instance and now we need to provide the possibility to filter/mask ... by taxon id (taxid) using the command line option (-window_masker_taxid) of BLAST (cf. http://www.ncbi.nlm.nih.gov/books/NBK1763/) before the job will be performed in one task. However searching in the documentation and the mailing list, I did not find anything about this. So it would be great to provide the possibility to subselect by taxid (e.g. NCBI BLAST server http://blast.ncbi.nlm.nih.gov/Blast.cgi) by changing the BLAST integration. We believe this could be of common interest. It would be great if anybody could comment on this. Thanks a lot, Thomas

3 4

shed tool dependencies
by Geert Vandeweyer 13 Feb '14

13 Feb '14

Hi, Is there a default notation to specify perl modules (threading modules) in a tool configuration or in a submission to the toolshed? I've got some tools to share that make extensive use of these modules, and they are not default in a perl distribution. Hence, I'd like to inform the users that they need to install these modules (or that they get installed by the the toolshed using cpan ?) Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer(a)ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

4 3

Several jobs stalled in the queue: Job runner assigned but no external ID recorded
by Derrick Lin 05 Feb '14

05 Feb '14

Hi guys, I have several jobs have been stuck in the queue for long time, I checked the handler log and found the following message: Job runner assigned but no external ID recorded, adding to the job handler queue Is there a way that I can clean these orphan jobs out of the queue? Cheers, Derrick

1 1

A new tool_data_table_conf.xml created under tool-data directory
by Derrick Lin 17 Jan '14

17 Jan '14

Hi guys, After installing the BWA from the Tools Shed, I find there is a new tool_data_table_conf.xml got created under tool-data directory. The file contains the entries of BWA's loc files. I believe the installed BWA still relies on the tool_data_table_conf.xml under galaxy root dir. Anyone can clarify what the one under tool-data dir is for? Regards, Derrick

3 7

FTP Problem: Users cannot see their uploads files.
by Misharl mon 07 Dec '13

07 Dec '13

Hi everybody, I have managed to get proftpd to work, it can connect to the galaxy sql database, and users can log to upload files in their directory. But there is a problem, when a galaxy user logs in the galaxy web platform, the user can't see his upload files since Galaxy doesn't have the rights to open the directory. How can i change the permissions in proftpd so that galaxy can open the user directory? Thanks in advance to all. Mish

4 17

Missing test results on (Test) Tool Shed
by Peter Cock 29 Nov '13

29 Nov '13

Hi Greg & Dave, I really like the new features on the (Test) Tool Shed for searching my repositories: * Latest revision missing tool tests * Latest revision failing tool tests * Latest revision all tool tests pass However there are some teething problems. Some of my tools are listed under "Latest revision failing tool tests", but when I go to look at them, no test results are shown (passing or failing): http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3 http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip In some cases there is indeed a failing test, for instance this is due to a bug in the test framework: http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go https://trello.com/c/KdGX3hkh And here there are missing dependencies (due to restrictive licensing problems): http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp https://trello.com/card/-/506338ce32ae458f6d15e4b3/770 Peter

4 77

Compressed data files in Galaxy? (e.g. GZIP or BGZF)
by Peter Cock 26 Nov '13

26 Nov '13

Hello all, What is the current status in Galaxy for supporting compressed files? We've talked about this before, for example in addition to FASTQ, many of us have expressed a wish to work with gzipped FASTQ. I understand that some have customized their local Galaxy installations to use gzipped FASTQ as a specific data type - I'm more interested in a general file format neutral solution. Also, I'd like to be able to used BGZF (not just GZIP) because it is better for random access - see for example http://blastedbio.blogspot.com/2011/11/bgzf-blocked-bigger-better-gzip.html - and makes it much easier to break up large datafiles for sharing over a cluster (i.e. it could be exploited in the current Galaxy code for splitting large sequence files). The 11 May 2012 Galaxy Development News Brief http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-May/009757.html mentions tabix indexing - that uses bgzip, so is there something general in place yet to allow tool wrappers to say they accept not just given file formats, but different compressed versions of file formats? Ideally I'd like to be able to write an XML tool description saying a tool produced BGZF compressed tabular data, or GZIP compressed Sanger FASTQ etc. Similarly, I'd like to specify my tool accepts FASTA or gzipped FASTA (including BGZF FASTA). While for older tools if they say they accept only uncompressed FASTA, Galaxy could automatically decompress any compressed FASTA entries in my history on demand. Peter

3 4

Samtools and idxstats
by Michiel Van Bel 20 Nov '13

20 Nov '13

Hi, I would like to inquire whether anyone has attempted to implement the idxstats tool from samtools into Galaxy? The xml-file for idxstats is not present in the Galaxy source code, which led me to try and implement it myself. However, the main problem I face is that the idxstats tool silently relies on having an index file available (within the same directory) for the bam file you which to print the stats for. E.g. samtools idxstats PATH/test.bam searches for PATH/test.bam.bai and gives an error when this file is not present. And somehow I cannot model this behavior in Galaxy. A different solution would of course be to ask the author(s) of samtools to have an option available where the user can directly indicate the path to the index file. regards, Michiel PS: I've searched the mailing list archives for this problem but did not find any matches. Apologies if I somehow missed the answer. -- ================================================================== Michiel Van Bel, PhD Expert Bioinformatician Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM mibel(a)psb.vib-ugent.be http://www.psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================

3 4

Tool unit tests using composite datatypes
by Peter Cock 18 Nov '13

18 Nov '13

Hello all, I'd like to be able to write some simple <test> entries for some of the BLAST+ tools using composite datatypes as input or output (i.e. small BLAST databases). This doesn't seem to be mentioned or hinted at on the wiki: http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax?action=show&redi… Is it possible to use a composite datatype as a test input? If so how? Normal datatypes are loaded into the test history using using the upload tool - does that mean I first need to extend the relevant datatypes to allow them to be uploaded? Example: Run blastp using a small query FASTA file and a small database, check the output (eg tabular). Is it possible to use a composite datatype as a test output? If so how? Example: Run makeblastdb using a small FASTA file, and check the output (a small BLAST database). Thanks, Peter

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Re: [galaxy-dev] Tool Shed packages for BLAST+ binaries
by Dave Bouvier 14 Nov '13

14 Nov '13

Peter, I apologize for the delay, here is the information you requested: ubuntu@ip-10-0-0-243:~$ uname -a Linux ip-10-0-0-243 3.8.0-25-generic #37-Ubuntu SMP Thu Jun 6 20:47:07 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux ubuntu@ip-10-0-0-243:~$ arch x86_64 ubuntu@ip-10-0-0-243:~$ echo $0 -bash --Dave B. On 08/26/2013 09:44 AM, Peter Cock wrote: > (Off list) > > Hi Dave, Greg, > > Just a reminder - without a bit more information about the Tool Shed > cluster I am stuck about how to debug this install issue. > > Thanks, > > Peter > > > On Wed, Aug 21, 2013 at 2:05 PM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote: >> On Wed, Aug 21, 2013 at 1:45 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote: >>> Peter, >>> >>> Here is the relevant log output for the installation of ncbi_blast_plus. A >>> quick google informs me that exit code 64 means "command line usage error", >>> for what it's worth. >>> >>> ... >>> tool_shed.util.shed_util_common DEBUG 2013-08-20 23:34:47,886 Adding new row >>> (or updating an existing row) for repository 'package_blast_plus_2_2_26' in >>> the tool_shed_repository table, status set to 'New'. >>> >>> Warning: local() encountered an error (return code 64) while executing ' >>> if [[ "$(uname)" == "Linux" ]]; then export >>> FILENAME="ncbi-blast-2.2.26+-ia32-linux.tar.gz"; fi && >>> if [[ "$(arch)" == "x86_64" ]]; then export >>> FILENAME="ncbi-blast-2.2.26+-x64-linux.tar.gz"; fi && >>> if [[ "$(uname)" == "Darwin" ]]; then export >>> FILENAME="ncbi-blast-2.2.26+-universal-macosx.tar.gz"; fi && >>> echo Fetching $FILENAME && >>> if [[ "$(uname)" == "Linux" ]]; then wget >>> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi && >>> if [[ "$(uname)" == "Darwin" ]]; then curl -O >>> ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi && >>> tar -zxvf $FILENAME && >>> echo Downloaded and decompressed >>> ' >>> >> >> Thanks Dave, >> >> I've made a note on this Trello card about exposing the log information >> of unsuccessful builds on the Tool Shed, >> https://trello.com/c/HVGrShnC/1042-tool-shed-should-test-installation-of-pa… >> >> Can you tell me what version of Linux this is, and which shell? >> >> $ uname >> ... >> >> $ arch >> ... >> >> $ echo $0 >> ... >> >> That might give me a clue about the nature of the failure. My >> hunch is that I am using something bash specific. >> >> The simplest solution would be if you could run each of these >> command by hand to see if it triggers the same error: >> >> if [[ "$(uname)" == "Linux" ]]; then export FILENAME="ncbi-blast-2.2.26+-ia32-linux.tar.gz"; fi >> if [[ "$(arch)" == "x86_64" ]]; then export FILENAME="ncbi-blast-2.2.26+-x64-linux.tar.gz"; fi >> if [[ "$(uname)" == "Darwin" ]]; then export FILENAME="ncbi-blast-2.2.26+-universal-macosx.tar.gz"; fi >> echo Fetching $FILENAME >> if [[ "$(uname)" == "Linux" ]]; then wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi >> if [[ "$(uname)" == "Darwin" ]]; then curl -O ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/$FILENAME; fi >> tar -zxvf $FILENAME >> echo Downloaded and decompressed >> >> Thanks, >> >> Peter

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galaxy-dev August 2013