August 2011 - galaxy-dev - lists.galaxyproject.org

samtools question
by Luciano Cosme 01 Aug '11

01 Aug '11

Hi Everyone, I am running galaxy locally (ubuntu 11.04) and I am having problem with samtools. When I am running TopHat I get an error message saying that could not locate samtools. Of course I did everything described in http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup Here is the error message: Error in tophat: [Mon Aug 1 13:03:53 2011] Beginning TopHat run (v1.3.1) ----------------------------------------------- [Mon Aug 1 13:03:53 2011] Preparing output location ./tophat_out/ [Mon Aug 1 13:03:53 2011] Checking for Bowtie index files [Mon Aug 1 13:03:53 2011] Checking for reference FASTA file Warning: Could not find FASTA file /tmp/tmpkcZN3L/dataset_26.dat.fa [Mon Aug 1 13:03:53 2011] Reconstituting reference FASTA file from Bowtie index Executing: /bin/bowtie-inspect /tmp/tmpkcZN3L/dataset_26.dat > ./tophat_out/tmp/dataset_26.dat.fa [Mon Aug 1 13:04:41 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Mon Aug 1 13:04:42 2011] Checking for Samtools Error locating program: samtools When I run "make" in the samtools directory I also get an error message: koala2@aedes:~/Desktop/galaxy/samtools$ make make[1]: Entering directory `/home/koala2/Desktop/galaxy/samtools' make[2]: Entering directory `/home/koala2/Desktop/galaxy/samtools' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o In file included from bgzf.c:36:0: bgzf.h:30:18: fatal error: zlib.h: No such file or directory compilation terminated. make[2]: *** [bgzf.o] Error 1 make[2]: Leaving directory `/home/koala2/Desktop/galaxy/samtools' make[1]: *** [lib-recur] Error 1 make[1]: Leaving directory `/home/koala2/Desktop/galaxy/samtools' make: *** [all-recur] Error 1 I also followed the installation guide from samtools, but did not work either. Unfortunately I found myself spending more time installing tools than using it. Yes I am a newbie. Thank you. Luciano

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3 ideas to improve the user experience for GALAXY
by 孙翰菲 01 Aug '11

01 Aug '11

Hi, I'm a user of Galaxy, I think Galaxy is a good idea except some small parts. 1. Progress Bar for uploading file I know that implement a progress bar for every tool is quite hard. But maybe it's not so hard for displaying the current percent of uploading, it's really helpful and comfortable for users (a countdown timer will be better). 2. Drag and Drop I've used gmail on my firefox, and I really like the function of "Drag & Drop" when I upload attachments. With this function, I can drag multiple small files (for example,'bed' files) in the special region of the page, which is easy to use. 3.Start automatically when uploading finished Some large files, need quite a long time before the uploading finished. We need to wait until the uploading is done because we cannot assign a task to an unfinished uploading file. Maybe we can pre-assign tasks for them, and we can go to other works when we finish doing this, because the operation will automatically apply to them when they have been uploading completely. I can imagine a story like this: I am quite tired after a whole day's busy work, but some sequencing data still need to be analyzed because I will show it to my boss tommorow. Then I think of GALAXY can do it well. I open the GALAXY, drag in several sequencing data, and assign a workflow to deal with the data in 2 minutes. Then I can go to sleep safely because GALAXY will run the workflow automatically when uploading is finished. When I get to GALAXY the next day, all the preliminary results are show on the page of GALAXY. I think it's really cool because it will reduce a lot of repetitive works for the user, and in my opinion, that is the REAL biology analysis platform. Best Wishes, Hanfei Sun

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GALAXY-GBROWSE : setting up incoming/outcomming functionalities (sharing data)
by BM 01 Aug '11

01 Aug '11

Hi, I am trying to set up the galaxy outgoing and incoming funtionalities in GBROWSE and GALAXY to send data between these applications. I have local instances of GALAXY and GBROWSE and I wonder how should I configure these. How this should look in the GBROWSE user interface (in the "share this track" section) ? How this should look in the GALAXY user interface ? My GBROWSE version : 2.38 and my GALAXY version : galaxy-galaxy-central-fd3391bcd903 Here the conf I set up : ------MY GALAXY SETTINGS------ I saw in a previous topic posted by nicki (http://gmod.827538.n3.nabble.com/Send-data-to-GBrowse-td2446346.html) that some files must be edtited : 1. universe_wsgi.ini I edited it as follows : GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt gbrowse_display_sites = wormbase,tair,modencode_worm,modencode_fly,yeast_sgd,perso 2. tool-data/shared/gbrowse/gbrowse_build_sites.txt I edited it as follows : #perso perso http://my_host.com/Gbrowse/cgi-bin/gbrowse_details/specie specie 3. datatypes_conf.xml I edited it as follows :  <display file="gbrowse/gbrowse_gff.xml" inherit="True" />  <display file="gbrowse/gbrowse_wig.xml" /> I have got the following files in "display_applications/gbrowse/" : gbrowse_gff.xml gbrowse_interval_as_bed.xml gbrowse_wig.xml ------MY GBROWSE SETTINGS------ I have edited the general section of "/var/www/GBROWSE/conf/specie.conf" according to the documentation http://gmod.org/wiki/GBrowse_Configuration_HOWTO#Track_Sharing_Options: [GENERAL] galaxy outgoing = http:/my_host.com:8080/tool_runner?tool_id=ncbi_blastn_wrapper galaxy incoming = https://my_host.com/Gbrowse/cgi-bin/gbgff ------------- First, I would like to look for the outgoing functionality from GBROWSE to GALAXY. Then, the incoming functionnality : from GALAXY to GBROWSE I hope someone can help me, I'm new to GALAXY. Thanks, greetings Ben

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