March 2012 - galaxy-dev - lists.galaxyproject.org

Error when installing galaxy
by Jemma Wu 28 Mar '12

28 Mar '12

Dear Galaxy developers, This is the first time that I installed Galaxy on a Debian Lenny 64 bit server. I got an error of "ImportError: No module named boto" when I ran %sh run.sh. Please see the error message of the installation output below: File "/home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 90, in app_factory add_ui_controllers( webapp, app ) File "/home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 39, in add_ui_controllers module = __import__( module_name ) File "/home/galaxy/galaxy-dist/lib/galaxy/web/controllers/cloud.py", line 9, in <module> import boto ImportError: No module named boto Does anyone know how to fix this error? Thanks in advance! Regards, Jemma

2 1

ImportError with galaxy
by Gilad Silberberg 28 Mar '12

28 Mar '12

Hi, I downloaded galaxy and tried to run fastq_paired_end_joiner.py. I got: File "/bubo/glob/g3/gilad/galaxy/tools/fastq/fastq_paired_end_joiner.py", line 3, in <module> from galaxy_utils.sequence.fastq import fastqReader, fastqNamedReader, fastqWriter, fastqJoiner ImportError: No module named galaxy_utils.sequence.fastq I tried changing PYTHONPATH in various ways, to: ./galaxy/lib or ./galaxy/lib/galaxy_utils or ./galaxy/lib/galaxy_utils/sequence but to no avail. My python version is 2.6.6. I would very much appreciate your help. Best, Gilad -- Gilad Silberberg Dept. of Molecular Biology& Functional Genomics Stockholm University Svante Arrheniusväg 20C 10691 Stockholm, Sweden Tel: +46-8-164135, Fax: +46-8-166488

1 0

Local galaxy cannot connect to local toolshed
by Joachim Jacob 28 Mar '12

28 Mar '12

Hi, I managed to run a local Tool Shed and add a repository. On the same machine, a local galaxy is running, and configured for using this local toolshed. In the Admin menu of Galaxy, I can see my local Toolshed listed under 'Search and Browse tool sheds'. However, when I click on my local toolshed entry, following connection error appears in the main window: This webpage is not available The webpage at*http://localhost:9009/repository/browse_valid_repositories?galaxy_url=http://192.168.10.24/&webapp=galaxy*might be temporarily down or it may have moved permanently to a new web address. Here are some suggestions: * Reload <http://localhost:9009/repository/browse_valid_repositories?galaxy_url=http:…>this web page later. Error 102 (net::ERR_CONNECTION_REFUSED): The server refused the connection. Thanks for the help, Joachim Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib

1 0

reload a tool's configuration from command line
by Tim-Christoph Roloff 28 Mar '12

28 Mar '12

Hello, I was wondering if there is a way to trigger the reload of a tool's configuration from command line. We are using a tool that loads .xml files from tool-data. The .xml files get modified by a script ran by cron frequently. Right now we reload the tool config via the admin interface but ideally we could integrate the reload in the cron job. Best regards Tim

4 3

Reducing costs in Cloud Galaxy
by Greg Edwards 28 Mar '12

28 Mar '12

Hi, I've got an implementation of some proteomics tools going well in Galaxy on AWS EC2 under Cloudman. Thanks for the help along the way. I need to drive the costs down a bit. I'm using an m1.large AMI and it's costing about $180 - $200 / month. This is about 55% storage and 45% instance costs. That's peanuts in some senses but for now we need to get it down so that it comes out of petty cash for the department, while the case is proven for it's use. I have a few questions and would appreciate ny insights .. 1. AWS has just released an m1.medium and m1.small instance type, which are 1/2 and 1/4 the cost of m1.large. http://aws.amazon.com/ec2/instance-types/ http://aws.amazon.com/ec2/pricing/ I tried the m1.small and m1.medium with the latest Cloudman AMI * *galaxy-cloudman-2011-03-22 (ami-da58aab3) All seemed to install ok, but the Tools took up tp 30 minutes to start execution on m1.medium, and never started on m1.small. m1.medium only added about 15% to run times compared with m1.large, can't say for m1.small. t1.micro does run (and for free in my Free Tier first year) but blows execution times out by a factor of about 3 which is too much. Has anyone tried these new Instance Types ? (m1.small/medium) 2. The vast majority of the storage costs are fro the Gemome databases in the 700GB /mnt/galaxyIndices, which I don't need. Can this be reduced to the bare essentials ? Using m1.small/medium and getting rid of the 700GB would being my costs down to say $50 / month which is ok. Thanks ! Greg E -- Greg Edwards, Port Jackson Bioinformatics gedwards2(a)gmail.com

2 3

Cufflinks inconsistency ...
by Johnson, Kory (NIH/NINDS) [C] 28 Mar '12

28 Mar '12

Hello, I performed 6 different runs of Cufflinks using the same Reference Annotation on 6 different samples. I expected the resulting tabular output to be constant given the same Reference Annotation was used each time. What I found is that there was an inconsistency. Specific example, here is top 5 rows from output for one of the six samples: tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage FPKM FPKM_conf_lo FPKM_conf_hi FPKM_status NM_001005484 - - NM_001005484 - - chr1:69090-70008 - - 0 0 0 OK NR_026820 - - NR_026820 - - chr1:34610-36081 - - 0 0 0 OK NM_001005221 - - NM_001005221 - - chr1:367658-368597 - - 0 0 0 OK NR_046018 - - NR_046018 - - chr1:11873-14408 - - 0 0 0 OK Here are top 5 rows from output for another of the six samples: tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage FPKM FPKM_conf_lo FPKM_conf_hi FPKM_status NM_001005484 - - NM_001005484 - - chr1:69090-70008 - - 0 0 0 OK NR_026820 - - NR_026820 - - chr1:34610-36081 - - 0 0 0 OK NM_001005221 - - NM_001005221 - - chr1:367658-368597 - - 0 0 0 OK NR_046018 - - NR_046018 - - chr1:11873-14408 - - 0 0 0 OK NR_024540 - - NR_024540 - - chr1:14361-29370 - - 15114.7 9501.21 20728.1 OK Here are top 5 rows from output for yet another of the six samples: tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage FPKM FPKM_conf_lo FPKM_conf_hi FPKM_status NR_026820 - - NR_026820 - - chr1:34610-36081 - - 0 0 0 OK NM_001005484 - - NM_001005484 - - chr1:69090-70008 - - 0 0 0 OK NM_001005221 - - NM_001005221 - - chr1:367658-368597 - - 0 0 0 OK NR_046018 - - NR_046018 - - chr1:11873-14408 - - 0 0 0 OK NR_024540 - - NR_024540 - - chr1:14361-29370 - - 28376.8 20008.9 36744.6 OK As a user, when selecting the same Reference Annotation to be used. I would expect the index of results by tracking id to be the same. Why is this happening? Why are they not consistent? If were to concat the above results across samples without correcting the indices, my data would be all mixed up. I bring this to your attention as someone may not correct the indices before concat and therefore would be doing downstream analysis incorrect concatted data. In turn, I would recommend that the index of results be corrected to be constant for a Reference Annotation when selected. Thank you in advance for this consideration. Best, Kory Johnson -------------------------------------------- Kory R. Johnson, MS, PhD Sr. Bioinformatics Scientist [cid:image001.jpg@01CD074F.C0C74CB0] www.kellygovernmentsolutions.com Providing Contract Services For: Bioinformatics Section, Information Technology & Bioinformatics Program, Division of Intramural Research (DIR), National Institute of Neurological Disorders & Stroke (NINDS), National Institutes of Health (NIH), Bethesda, Maryland Mailing Address: NINDS/NIH Clinical Center (Building 10) Office 5S223 9000 Rockville Pike Bethesda, MD 20892 Contact Information: Phone: 301-402-1956 Fax: 301-480-3563 email: johnsonko(a)ninds.nih.gov P Green Message: Please consider the environment before printing this e-mail. Thank you. Important Message: This electronic message transmission contains information intended for the recipient only. Such that, the information contained herein may be confidential, privaledged, or proprietary. If you are not the intended recipient, be aware that any disclosure, copying, distribution, or use of this information is strictly prohibited. If you have received this electronic information in error, please notify the sender immediately by telephone. Thank you. --------------------------------------------

2 1

Formatting has lost the "horizontal rule" dividers in new Galaxy style
by Greg Edwards 28 Mar '12

28 Mar '12

Hi, I reinstalled and updated my Cloud Galaxy on AWS today and picked up a New Look. Same as the public site, https://main.g2.bx.psu.edu. Like it ! but I have noticed a couple of small formatting chnages in the "docutils" controls. 1. The horizontal rule dividers specified by a "-----" in the text have disappeared. 2. Also I spotted a change where this .. *- line 1 of some bullets* *- line 2 of some bullets* * * *Following line*. .. lost the blank line after the "line 2" line. The fixed-width Courier text looks great now, larger and antialiased, at least in my Chrome on Mac. That's all from the Pedantic Dept. Cheers, -- Greg Edwards, Port Jackson Bioinformatics gedwards2(a)gmail.com

2 2

Possible bug: Tags in a workflow gets duplicated hundreds of times
by Anthonius deBoer 28 Mar '12

28 Mar '12

Hi, I have run into an issue with a tag being duplicated hundreds of times each time I open, edit or clone a workflow. I have tried to manually remove them, but each time the tag gets inserted somehow and duplicated each time I edit the workflow. By now there are hundreds of copies of the tags at it makes loading and running the workflow very slow. Is there a way to remove a tag from the system somehow? I am willing to dig into the database with some SQL statement but not sure where to start... Thanks Thon

3 2

Getting the input name of the dataset
by diana michelle magbanua 28 Mar '12

28 Mar '12

Hi there, I am new to Galaxy and I've just recently learned how to integrate a Perl script to it. Now, my code uses the input file's name as a header for a column in the output. When I ran it in Galaxy, I did get the filename, but it's the one ending in .dat (actually, I got the entire path of the file). I was wondering if it's possible to retain the original name of the file (or retrieve the name of the input dataset) and use it in the output file. I can't think of a Perl script for this yet, for my scripting's a bit rusty (I just started learning Perl last month). I've already checked the FAQs page, the wiki and the mailing list, but I did not get any useful hints. I hope my writing made sense. Thank you for your time! - Diana

2 1

Error for draw quality score boxplot
by Xu, Jianpeng 27 Mar '12

27 Mar '12

Hi, I have installed the local galaxy and tried to run draw quality score boxplot. It showed the error message: Could not find/open font when opening font "arial", using internal non-scalable font Could you please tell me how to fix it ? Thanks, Jianpeng ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

2 1