Re: [galaxy-user] Error installing MACS on local Galaxy
Hi Jennifer, I am now trying to run MACS 1.3.7.1. in Galaxy. I also ran python setup.py install and set variables $PATH and $PYTHONPATH for the commandline run. Nevertheless, MACS gives error: /ImportError: No module named MACS.OptValidator/ I checked - library OptValidator.py exists in the file system, and path to the folder is both in $PATH and $PYTHONPATH Any ideas? best regards, Jerzy On 10/17/2012 04:18 PM, Jennifer Jackson wrote: Hello Jerzy, The MACS wrapper in Galaxy currently supports version 1.3, which explains the problems with 1.4. Tool dependencies are noted on this wiki: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies For the other errors, are you trying to run MACS on the command line or within Galaxy? For command line, some environment variables need to be set up, the MACS documentation has the details: http://liulab.dfci.harvard.edu/MACS/INSTALL.html Hopefully this helps, Jen Galaxy team On 10/17/12 2:09 AM, Jerzy Dyczkowski wrote: Hello, I cannot run MACS on the local Galaxy. When I install MACS version 1.4., it gives error something like cannot find macs. When I install version 1.3.7.1 it gives error /line 34, in module from MACS.OptValidator import opt_validate ImportError: No module named MACS.OptValidator/ I sourced PATH to the directory with this module. Any ideas? best regards, Jerzy -- Dr Jerzy Dyczkowski Bioinformatician Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Grisebachstr. 5 D-37077 Göttingen Email:jerzy.dyczkow...@eni-g.de Phone: +49 (0)551 39-12352 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Dr Jerzy Dyczkowski Bioinformatician Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Grisebachstr. 5 D-37077 Göttingen Email: jerzy.dyczkow...@eni-g.de Phone: +49 (0)551 39-12352 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Error installing MACS on local Galaxy
Hello, I cannot run MACS on the local Galaxy. When I install MACS version 1.4., it gives error something like cannot find macs. When I install version 1.3.7.1 it gives error /line 34, in module from MACS.OptValidator import opt_validate ImportError: No module named MACS.OptValidator/ I sourced PATH to the directory with this module. Any ideas? best regards, Jerzy -- Dr Jerzy Dyczkowski Bioinformatician Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Grisebachstr. 5 D-37077 Göttingen Email: jerzy.dyczkow...@eni-g.de Phone: +49 (0)551 39-12352 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Upload data to local Galaxy by copying them to the file folder
Hello, How to put data to the local Galaxy server via ftp, ssh or copying directly to some subfolder in galaxy-dist? We installed a local Galaxy instance and it is running. Manual uploading files from user PCs is slow due to less than perfect connections in the local network. We would prefer uploading large files by ssh from the central cluster to the server on which Galaxy is running. I can conect to the Galaxy server and Galaxy folder structure, however, I cannot find where to put files. Are they all renamed and coded as something like: galaxy-dist/database/files/000/dataset_38.dat ? The option of uploading via ftp on main.g2.bx.psu.edu is absent in local Galaxy distribution. best regards, Jerzy ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-user] Extracting number of reads from Bowtie analysis
Hello, I am new here! I am aligning Solexa files to genome using tool: NGS: Mapping: Map with Bowtie for Illumina. My question: What is the most easy way to check the number of aligned reads in the output from above? I couldn't find this number directly. I found a way, but it looks circular and unoptimal: to run Bowtie with option: put umapped reads into the file, download the file, open it, count reads, subtract from reads in the original file. However, downloading large files is time-consuming, and I am sure the easier way is somewhere. Further question: good link to help on how to improve number of reads from ChIP study aligned to mouse genome would be also appreciated. best regards, Jerzy ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
