[galaxy-dev] Galaxy Community Conference Early Registration Deadline extended to May 1
Hello all, The early registration deadline for the 2011 Galaxy Community Conference has been extended by a week, from April 24 to May 1. The conference is being held in Lunteren, the Netherlands, 25-26 May, with a special Introduction to Galaxy session on the evening of May 24. That's the good news. The bad news is that online registration has been taken offline, starting today, until April 26 or 27. We took this step because of unexpectedly high demand for conference centre hotel rooms on May 24 and 26. We still have ample rooms for the night of May 25,* but we are now sold out on the other nights*. We are working with the conference centre to increase our room allotment on May 24 and 26. We are optimistic of getting more rooms on May 26, but we are not as hopeful about getting additional rooms for May 24. We will reopen registration next Tuesday or Wednesday and post an update on the room situation, including alternatives, at that time. As always, please let me know if you have any questions. Thanks for your patience, Dave C. -- http://galaxy.psu.edu/gcc2011/ http://getgalaxy.org http://usegalaxy.org/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Could anyone body tell me why our C program do not work in galaxy
Dear Sir, We have a program writen in C lanuage. It can run nomally in linux environment. We plan to add it to galaxy, but it did not work. The C file after complie named shortest-path The shortest-path.xml is as follow: Could anybody tell me what is wrong ? why it does not work? Thank you very much! Best Wishes! Yan-Hui Li tool id=shortest_path_1 name=shortest_path command interpreter=C./shortest_path $infile1 $output /command inputs param format=text name=infile1 type=data label= expressed_genes_20101024.hprd8_biogrid-2.0.58.adj_matrix.txt / /inputs outputs data format=tabular name=output / /outputs tests test param name=input value=1/ param name=input value=../GEO_dataset/expressed_genes_u133a.6k_u133p2.8k_20101024.txt/ param name=input value=../ppi/hprd8_biogrid-2.0.58.ppi.txt/ output name=out_file1 file=expressed_genes_20101024.hprd8_biogrid-2.0.58.ppi.txt/ /test /tests /tool ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Could anyone body tell me why our C program do not work in galaxy
Without seeing an error message I'll guess that issue is that there is no C interpreter. Your program is a compiled executable. Try the following and let me know (including any error messages) if it doesn't work: command shortest_path $infile1 $output /command -Dannon On Apr 22, 2011, at 2:12 AM, liyanhui607 wrote: Dear Sir, We have a program writen in C lanuage. It can run nomally in linux environment. We plan to add it to galaxy, but it did not work. The C file after complie named shortest-path The shortest-path.xml is as follow: Could anybody tell me what is wrong ? why it does not work? Thank you very much! Best Wishes! Yan-Hui Li tool id=shortest_path_1 name=shortest_path command interpreter=C./shortest_path $infile1 $output /command inputs param format=text name=infile1 type=data label= expressed_genes_20101024.hprd8_biogrid-2.0.58.adj_matrix.txt / /inputs outputs data format=tabular name=output / /outputs tests test param name=input value=1/ param name=input value=../GEO_dataset/expressed_genes_u133a.6k_u133p2.8k_20101024.txt/ param name=input value=../ppi/hprd8_biogrid-2.0.58.ppi.txt/ output name=out_file1 file=expressed_genes_20101024.hprd8_biogrid-2.0.58.ppi.txt/ /test /tests /tool 体验网易邮箱2G超大附件，轻松发优质大电影、大照片，提速3倍! ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Could anyone body tell me why our C program do not work in galaxy
2011/4/22 liyanhui607 liyanhui...@163.com: Dear Sir, We have a program writen in C lanuage. It can run nomally in linux environment. We plan to add it to galaxy, but it did not work. The C file after complie named shortest-path The shortest-path.xml is as follow: Could anybody tell me what is wrong ? why it does not work? Thank you very much! Best Wishes! Yan-Hui Li What error message do you get? Did you try the two changes I suggested (the same things Dan just suggested as well): https://bitbucket.org/galaxy/galaxy-central/issue/525 Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Special considerations for installing local instance of Galaxy on Mac OS X (10.6.7)?
Hi Everyone, I'm having trouble getting some of the tools to work on my local installation of Galaxy on a Mac (OS X version 10.6.7). The instructions on the GetGalaxy wiki are clear, and I was able to download and install from the anonymous Mercurial repository. Galaxy starts up and runs just fine for tools like Get Data, FASTQ Groomer, and FASTQ Summary Statistics. The problems started when I try to run Graph/Data Display - Boxplot (GnuPlot). I get the error: An error occurred running this job:/bin/sh: gnuplot: command not found Error running gnuplot. The FASTX Barcode Splitter also gives me an error: An error occurred running this job:/Users/Me/galaxy-dist/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh: line 65: fastx_barcode_splitter.pl: command not found zcat: /Users/Me/galaxy-dist/database/files/000/dataset_10.dat.Z: No such file or directory sed: illegal opt I'm assuming these are Tool Dependency problems, although I have tried to install the OS X versions of GnuPlot and the FASTX Toolkit and still get errors. Are there any suggestions from users who are successfully running Galaxy on OS X? Thanks in advance, Jeff ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
