February 2012 - galaxy-user - lists.galaxyproject.org

snpEff: html report is not displaying after update
by Praveen Raj Somarajan 22 Feb '12

22 Feb '12

Hi All, I updated galaxy recently to the latest version. Everything looks fine, except snpEff report html view. It was displaying properly (all tables and summary values) before the update, but the summary values are not displaying after the update. A sample screen-shot is attached for your reference. Could you please figure out this issue? When I ran the same on command line, the reports were generated correctly. I assume, something (datatypes or preview) has changed by the update. Please let me know the work around on this? Secondly, as we know, snpEff also generates a gene-wise annotation file along with other results, but somehow we cannot access this file through Galaxy. Though we see the link in the html report, but it seems the path is broken. Let me know your suggestions. Best, Raj ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD

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galaxy - table browser fasta and bed format
by Rita Rebollo 22 Feb '12

22 Feb '12

Hello, I got an unexpected scientific result from a simple "get data" from UCSC table browser with galaxy. I have uploaded the mouse mm9 repeat masker track with a filtering on repClass = LINE SINE LTR DNA If I ask the output to be sequences, I will get 1 454 739 sequences, but if I ask the same data to be retrieved as a BED format I get roughly 3 600 000 which is the closest to the "summary/statiscs" of the dataset (item count = 3 493 484). Why is there a difference between the FASTA file and the BED file? Thank you Rita

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Galaxy not accessed from network
by Cai Shaojiang 22 Feb '12

22 Feb '12

Dear all, I just installed Galaxy on our server. It works when I typed in http://localhost:8080/ on the server itself. But when I want to access it from another PC, it fails. I try the host name and the IP of the server, but both of them failed. Currently we have other web applications running on port 80 of the server. They are working well. Could anybody please indicate where could be the probable problem? Thanks. -- Cai Shaojiang Department of Information Systems, School of Computing, National University of Singapore Tel: +65-65167355

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Cufflinks related problem
by Bomba Dam 22 Feb '12

22 Feb '12

Dear Noa, Can you please tell me the parameters that I should keep while mapping bacterial transcripts using cuffkins. I have kept the default parameters as in Cufflinks and used my custom genome annotation in gff3 format. The cufflinks seems to work Ok but all the FPKM values in these files are zero. As suggested by other users I have checked the correctness of my GFF3 files. The corresponding fasta file was used for mapping the transcripts using Bowtie. Are there any special trick for mapping bacterial transcriptome. regards, Bomba

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R scripts for DESeq
by Liusong Yang 21 Feb '12

21 Feb '12

Hello, I am planning to put DESeq into galaxy. I am a newcomer for both Galaxy and R. I have already read all of the related discussion in this group. I also noticed that there are r_wrapper.sh and DESeq.xml added into galaxy recently under the path of tools. These lines are from r_wrapper.sh. ### Run R providing the R script in $1 as standard input and passing ### the remaining arguments on the command line I guess this means we need to give the DESeq R script to the wrapper as standard input. My question is where or what is the DESeq R scripts? I installed R and DESeq package, but I can not fund anything like DESeq.R or something similar? I feel so confusing now. Any comments or suggestions would be absolutely appreciated! Thanks Lisa

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Megablast
by Scott Tighe 21 Feb '12

21 Feb '12

Hi Galaxy users When Magablasting 1)....what does the "identity value -p" mean ...is it percent identity? I want my megablast results to be reported form only a 100% match. I do not see a place for % alinement concordance. 2) form my Illumina Hiseq reads, are the adaptor sequences filtered during the filter step? Scott tighe --2 Scott Tighe Advanced Genome Technology Lab Vermont Cancer Center at the University of Vermont 149 Beaumont Avenue Health Science Research Bd RM 305 Burlington Vermont USA 05405 lab 802-656-AGTC (2482) cell 802-999-6666

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about primer/adaptor removal?
by Hao Zheng 21 Feb '12

21 Feb '12

Hi, Does galaxy provide primer/adaptor removal for NGS (illumina) reads? Thanks. Arthur

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ftp Server unavailable
by Florian Peschke 21 Feb '12

21 Feb '12

2 1

upgrade script
by Victor Ruotti 21 Feb '12

21 Feb '12

Hi, I'm trying to use the upgrade script given that the current schema is now version 90. I get the following error. Can anyone point me out, maybe there is something to do before upgrading? thanks in advance. Victor ----------------trying to start galaxy I get Traceback (most recent call last): File "/opt/galaxy/galaxy-dist-original/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/opt/galaxy/galaxy-dist-original/lib/galaxy/app.py", line 32, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) File "/opt/galaxy/galaxy-dist-original/lib/galaxy/model/migrate/check.py", line 105, in create_or_verify_database % ( db_schema.version, migrate_repository.versions.latest, config_arg ) ) Exception: Your database has version '90' but this code expects version '79'. Please backup your database and then migrate the schema by running 'sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade'. Removing PID file runner0.pid --------------trying to upgrade sh manage_db.sh -c ./universe_wsgi.runner.ini upgrade Traceback (most recent call last): File "./scripts/manage_db.py", line 63, in <module> main( repository=repo, url=db_url ) File "/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/shell.py", line 150, in main ret = command_func(**kwargs) File "/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 221, in upgrade return _migrate(url, repository, version, upgrade=True, err=err, **opts) File "/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/api.py", line 327, in _migrate changeset = schema.changeset(version) File "/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py", line 173, in changeset changeset = self.repository.changeset(database, start_ver, version) File "/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/repository.py", line 170, in changeset changes = [self.version(v).script(database, op) for v in versions] File "/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/repository.py", line 145, in version return self.versions.version(*p, **k) File "/opt/galaxy/galaxy-dist-original/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/version.py", line 125, in version return self.versions[VerNum(vernum)] KeyError: <VerNum(90)>

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galaxy - table browser fasta and bef format
by Rita Rebollo 20 Feb '12

20 Feb '12

Hello, I got an unexpected scientific result from a simple "get data" from UCSC table browser with galaxy. I have uploaded the mouse mm9 repeat masker track with a filtering on repClass = LINE SINE LTR DNA If I ask the output to be sequences, I will get 1 454 739 sequences, but if I ask the same data to be retrieved as a BED format I get roughly 3 600 000 which is the closest to the "summary/statiscs" of the dataset (item count = 3 493 484). Why is there a difference between the FASTA file and the BED file? Thank you Rita

1 0