February 2013 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] DustMasker tool for ncbi_blast_plus
by Nicola Soranzo 15 Feb '13

15 Feb '13

Adding galaxy-dev list in CC as suggested by Peter. Il giorno mer, 06/02/2013 alle 16.57 +0000, Peter Cock ha scritto: > On Tue, Feb 5, 2013 at 11:45 AM, Nicola Soranzo <soranzo(a)crs4.it> wrote: > > Dear Peter, > > I have created a simple Galaxy tool for DustMasker of the NCBI BLAST+ > > suite, which I think would be a useful addition to the ncbi_blast_plus > > repository you're maintaining in the Galaxy Tool Shed. > > > > You can find it and hopefully pull it from: > > > > https://bitbucket.org/nsoranzo/ncbi_blast_plus > > > > Kind regards, > > Nicola > > Hi Nicola, > > Thanks for getting involved - we can discuss this on the galaxy-dev > mailing list if you prefer? For now I have CC'd Edward Kirton as he > is/was working on masking in BLAST databases for Galaxy. > > I can see the new file > tools/ncbi_blast_plus/ncbi_dustmasker_wrapper.xml however it refers to > multiple new file formats - where are they defined? > > * acclist > * maskinfo_asn1_bin > * maskinfo_asn1_text > * seqloc_asn1_bin > * seqloc_asn1_text Hi Peter, I added these file formats mostly as placeholders for a future implementation. Now I have changed a bit the tool by removing acclist and seqloc_xml formats since they are not recognized by the last versions of dustmasker (I also sent an email to blast-help(a)ncbi.nlm.nih.gov to inform them of this bug). As before, you can find the new version at: https://bitbucket.org/nsoranzo/ncbi_blast_plus I stripped the old commit and did a new one, not a very good practice, sorry about that. > Have you looked at the (commented out) bits in the makeblastdb wrapper > which would perhaps be relevant? This is something Edward Kirton wrote > which I haven't integrated yet: > >  >  > > Perhaps all you need to offer in ncbi_dustmasker_wrapper.xml is > 'fasta' and 'asnb' (binary ASN) formats? Edward - did you have an > 'asnb' definition? 'fasta' and 'interval' are the ones I'm interested for my use case. 'maskinfo_asn1_bin' is probably the one referenced as 'asnb' in the cited code (ASN1 is a general data serialization format like XML). A file in this format can be given as input to "makeblastdb -mask_data". Nicola -- Nicola Soranzo, Ph.D. CRS4 Bioinformatics Program Loc. Piscina Manna 09010 Pula (CA), Italy http://www.bioinformatica.crs4.it/

2 4

Install NGSRich in local galaxy
by Hakeem Almabrazi 15 Feb '13

15 Feb '13

HI, Does anyone know who to install NGSRich software on a local instance of Galaxy? I tried to install it from the shed_tool but it does not show up in the repository, so I manually downloaded it from http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=name&operatio… But now, I am not sure how to add it into my galaxy env. Any help will be highly appreciated ... Regards,

2 4

Confusion on Updating Code
by greg 15 Feb '13

15 Feb '13

Hi guys, I'm trying to do my first update on my local galaxy install (it's been a few months at least since I installed) I'm trying to follow the instructions here to update the code: http://wiki.galaxyproject.org/Admin/Get%20Galaxy#Keep_your_code_up_to_date My first question is how do I roll back if something goes wrong in the upgrade? My second question is that this page http://wiki.galaxyproject.org/DevNewsBriefs/2013_02_08 says that I need to do something to get onto the stable branch? Right now when I run hg branch it says default. I'd prefer to be on stable. Any idea what I should do? (and again how can I roll back to the code i have now if something goes wrong?) Thanks, Greg Summary information: [galaxy@vm244]/usr/local/galaxy/galaxy-dist>hg summary parent: 7986:12fcd068b12e tip Do not hide failed datasets with HideDatasetAction post job action. branch: default commit: 3721 modified, 9 unknown update: (current)

2 3

Problem using NGS: Peak Calling - MACS
by greg 15 Feb '13

15 Feb '13

Hi guys, I'm trying to run MACS in my local galaxy install (see screenshot: http://snag.gy/5QGUH.jpg) And I'm getting this error: Usage: macs <-t tfile> [-n name] [-g genomesize] [options] Example: macs -t ChIP.bam -c Control.bam -f BAM -g h -n test -w --call-subpeaks macs: error: no such option: --lambdaset Thanks in advance for any help. -Greg Here's how I installed Macs (I guess it doesn't come built in?) > cd /usr/local/galaxy/downloads/ > wget https://github.com/downloads/taoliu/MACS/MACS-1.4.2-1.tar.gz > tar -xzvf MACS-1.4.2-1.tar.gz > cd MACS-1.4.2 > source /usr/local/galaxy/job_environment_setup_file > python setup.py install > deactivate > cd /misc/local/galaxy/galaxy_python/bin > ln -s macs14 macs (and made sure /misc/local/galaxy/galaxy_python/bin is on the galaxy user's path)

3 7

Error while writing data in tophat2
by Sachit Adhikari 15 Feb '13

15 Feb '13

Galaxy is working fine in command line whereas in Galaxy at last i got this error: [2013-02-15 01:39:12] Reporting output tracks [FAILED] Error running /usr/local/bin/tophat_reports --min-anchor 8 --splice-mismatches 0 --min-report-intron 50 --max-report-intron 500000 --min-isoform-fraction 0.15 --output-dir ./tophat_out/ --max-multihits 20 --max-seg-multihits 40 --segment-length 25 --segment-mismatches 2 --min-closure-exon 100 --min-closure-intron 50 --max-closure-intron 5000 --min-coverage-intron 50 --max-coverage-intron 20000 --min-segment-intron 50 --max-segment-intron 500000 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 --read-realign-edit-dist 3 --max-insertion-length 3 --max-deletion-length 3 -z gzip -p4 --no-closure-search --no-coverage-search --no-microexon-search --sam-header ./tophat_out/tmp/genome_genome.bwt.samheader.sam --report-discordant-pair-alignments --report-mixed-alignments --samtools=/bin/samtools --bowtie2-max-penalty 6 --bowtie2-min-penalty 2 --bowtie2-penalty-for-N 1 --bowtie2-read-gap-open 5 --bowtie2-read-gap-cont 3 --bowtie2-ref-gap-open 5 --bowtie2-ref-gap-cont 3 /data/rathi/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome.fa ./tophat_out/junctions.bed ./tophat_out/insertions.bed ./tophat_out/deletions.bed ./tophat_out/fusions.out ./tophat_out/tmp/accepted_hits ./tophat_out/tmp/left_kept_reads.bam Loading ...done Is it a known bug?

2 3

Re: [galaxy-dev] hg19 reference gnome for Tophat2
by Jeremy Goecks 15 Feb '13

15 Feb '13

Now try running the test data in Galaxy to see if you get the same results. You should probably try running from the history first and then try adding the test data as a built-in genome via the bowtie2_indexes.loc table Best, J. On Feb 15, 2013, at 12:18 AM, Sachit Adhikari wrote: > Hi Jeremy, > > I was successfully able to run the test data from the tophat2 website in command line. I think there's something wrong with the reference genome. I have correctly specified the path of reference genome? What's the problem I am facing? > > On Thu, Feb 14, 2013 at 1:44 PM, Jeremy Goecks <jeremy.goecks(a)emory.edu> wrote: > Try using the Tophat test data to verify your installation; it's known to have splice junctions: > > http://tophat.cbcb.umd.edu/tutorial.html > http://tophat.cbcb.umd.edu/downloads/test_data.tar.gz > > Good luck, > J. > > On Feb 14, 2013, at 6:29 AM, Sachit Adhikari wrote: > >> I tried with many data but still the same problem and regarding settings I haven't changed a thing of Tophat2. What might be causing this error? >> >> Thanks >> >> On Wed, Feb 13, 2013 at 7:10 PM, Jeremy Goecks <jeremy.goecks(a)emory.edu> wrote: >> If the other outputs are fine, then the problem is likely with your data and/or your Tophat settings. >> >> Good luck, >> J. >> >> On Feb 13, 2013, at 8:22 AM, Sachit Adhikari wrote: >> >>> Ok sorry. I did that, but the output of splice junctions is empty. The other outputs looks fine. What might be the problem? >>> >>> Thanks, >>> >>> Sachit >>> >>> On Wed, Feb 13, 2013 at 1:20 PM, Jeremy Goecks <jeremy.goecks(a)emory.edu> wrote: >>> > Shall I replace: >>> > >>> > /orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 >>> > >>> > with >>> > >>> > hg19 hg19 hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index >>> >>> Yes, that's correct. >>> >>> Finally, please email only galaxy-dev with questions about local installations; galaxy-user is for questions about how to use Galaxy. >>> >>> Best, >>> J. >>> >>> >> >> > >

1 0

History does not automatically update anymore
by Anthonius deBoer 15 Feb '13

15 Feb '13

Hi, I have noticed that in the latest version of galaxy-dist, my history does not automatically update anymore. I have to press the refresh circle to have it update... I did change my proxy setup a little, so it would no longer require API calls to be authenticated, while access through the frontend would still require that so it may have something to do with that, but just wanted to check if others see this issue... I will send out my proxy settings in a later email, since it may help people that are struggling with the same... Thon

2 2

Bug in Galaxy Reports tool
by Joachim Jacob |VIB| 15 Feb '13

15 Feb '13

Hi all, Running ~/galaxy-dist/run_reports.sh brings up the Galaxy Reports interface on poort 9001. When clicking on 'Jobs per user' -> picking a user -> picking a month -> and clicking on 'State' in the bar at the top, clears the screen. Thanks, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

3 3

Setting up a proxy with authentication while waiving this for API calls
by Anthonius deBoer 15 Feb '13

15 Feb '13

Hi, I have been struggling with setting up my galaxy system to allow it to use the LDAP authentication for users that come in through the frontend, while not wanting to have to use authentication when user want to access through the API....I found some solution and I thought I'd share it with the world so that people may learn from this and maybe also tell me if I am doing something wrong, or worse, insecure! I setup two web servers in the universe file at localhost:8080 and localhost:8081. For the one at 8080 i require authentication, for the one at 8081 I do not in the settings for apache proxy server shown below.... The I setup a ReWriteRule for anything addressed to /api/ and route that to the one at 8081, that does not require authentication, while everything else goes through 8080 which does... It seems to work nicely, although I have a nagging feeling this leaves open some backdoors somewhere, but please tell me if I do... <code> <Directory /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static> Options FollowSymLinks Order Allow,Deny Allow from all </Directory> <Proxy http://localhost:8080> AuthType Basic AuthName "GALAXY@GHI. Please log in with your Windows account" AuthBasicProvider ldap AuthLDAPURL "ldap://__YOUR_LDAP_SERVER/ou=Users - Employees,dc=genomichealth,dc=com?sAMAccountName?sub?(objectClass=*)" AuthzLDAPAuthoritative off AuthLDAPBindDN __USERNAME__ AuthLDAPBindPassword __PASSWORD Require valid-user RequestHeader set REMOTE_USER %{AUTHENTICATE_SAMACCOUNTNAME}e </Proxy> #Extended the timeout since some GALAXY actions can take a long time TimeOut 60000 RewriteEngine on ReWriteRule ^(/api/.*) http://localhost:8081$1 [L] RewriteRule ^/static/style/(.*) /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/static/scripts/(.*) /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/static/(.*) /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/$1 [L] RewriteRule ^/favicon.ico /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/favicon.ico [L] RewriteRule ^/robots.txt /mnt/ngs/analysis/svcgalaxy/galaxy-dist/static/robots.txt [L] RewriteRule ^/admin/jobs(.*) http://localhost:8079/admin/jobs$1 [P] RewriteRule ^(.*) http://localhost:8080$1 [P] </code> Thon

1 1

Why are the search options in datasets no longer using AND logic?
by Anthonius deBoer 14 Feb '13

14 Feb '13

Hi, One very cool feature was to be able to search quickly for datasets using the search feature. You could continue to add terms until your search results in the correct set... It was basically doing an AND search for the terms you entered..... This feature has seem to have disappeared? Now a search term replaces your previous term so you can no longer pair your search down and there does not seem to be any support for using AND or &.... Is this a bug or a new feature? Thanks Thon

2 1