Hi again, I didn’t get any response to this so decided to try an upgrade in the hope that I could reestablish access to the toolshed. I used bitbucket because I was unsure of the implications if I moved to github. Here are the commands I issued:
su – galaxy cd /galaxy/galaxy-dist/ hg pull hg update latest_15.05 I was repeatedly asked questions re changing or deleting various scripts: local changed static/scripts/packed/mvc/data.js which remote deleted use (c)hanged version or (d)elete? C I chose c for all of these Once that finished, the merging process began but eventually ended in an error message: merging static/scripts/nls/zh/locale.js abort: could not symlink to './': File exists: /galaxy/galaxy-dist/static/scripts/packed Any help with this error would be greatly appreciated. Last time I updated, I did this from within the galaxy-dist directory (/galaxy/galaxy-dist) rather than the root /galaxy directory and it worked. Is that correct? Regards, Eleanor Eleanor Morgan Senior Scientific Officer | School of Biomedical Sciences | Faculty of Health Sciences Curtin University Tel | +61 8 9266 7516 Mob | +61 408 004 369 Fax | +61 8 9266 2342 Email | e.mor...@curtin.edu.au<mailto:e.mor...@curtin.edu.au> Web | biomed.curtin.edu.au [cid:8FD8F6A6-991E-469B-899B-F84FF0A57C2A] Curtin University is a trademark of Curtin University of Technology. CRICOS Provider Code 00301J (WA), 02637B (NSW) From: Eleanor Morgan <e.mor...@curtin.edu.au<mailto:e.mor...@curtin.edu.au>> Date: Tuesday, 19 May 2015 9:50 pm To: "galaxy-...@lists.bx.psu.edu<mailto:galaxy-...@lists.bx.psu.edu>" <galaxy-...@lists.bx.psu.edu<mailto:galaxy-...@lists.bx.psu.edu>> Subject: [galaxy-dev] tophat2 failing to execute Hello, I am running a local Galaxy install, last update was June, 2014 release. I installed Tophat2 from the tool repository some months ago and the tool dependency packages for Bowtie2 and Samtools were also installed. I have built bowtie2 indices on the human hg19 genome and can select this as the reference genome. I am working through a tutorial with paired-end sequence reads that works fine on the main galaxy public server. When I try to run it on my local instance, however, Tophat2 fails. The error reported in the galaxy data window is: Fatal error: Tool execution failed [2015-05-19 21:15:11] Beginning TopHat run (v2.0.9) ----------------------------------------------- [2015-05-19 21:15:11] Checking for Bowtie Bowtie version:2.1.0.0 [2015-05-19 21:15:11] Checking for Samtools S I checked the tool_dependency.xml file <tool_dependency> <package name="bowtie2"version="2.1.0"> <repository changeset_revision="017a00c265f1"name="package_bowtie2_2_1_0"owner="devteam"prior_installation_required="False"toolshed="http://toolshed.g2.bx.psu.edu"; /> </package> <package name="samtools"version="0.1.18"> <repository changeset_revision="171cd8bc208d"name="package_samtools_0_1_18"owner="devteam"prior_installation_required="False"toolshed="http://toolshed.g2.bx.psu.edu"; /> </package> <package name="tophat2"version="2.0.9"> <repository changeset_revision="8549fd545473"name="package_tophat2_2_0_9"owner="devteam"prior_installation_required="False"toolshed="http://toolshed.g2.bx.psu.edu"; /> </package> </tool_dependency> All of the listed packages appear to be installed. I am unsure why in the run log it is checking for Bowtie instead of Bowtie2, although the version is correct for the Bowtie2 package that is installed. I would like to reinstall everything, but can’t get onto the toolshed anymore, I just get a message that I will be redirected, but nothing happens. I am a newbie user of galaxy. Can anyone direct me to a log file that might contain more information about why Tophat2 is failing to execute? It works fine on the command line. Thanks very much for any advice on what I should check next. Regards, Eleanor Eleanor Morgan Senior Scientific Officer | School of Biomedical Sciences | Faculty of Health Sciences Curtin University Tel | +61 8 9266 7516 Mob | +61 408 004 369 Fax | +61 8 9266 2342 Email | e.mor...@curtin.edu.au<mailto:e.mor...@curtin.edu.au> Web | biomed.curtin.edu.au [cid:73AB5085-67E7-491A-AC7A-694821970AA3] Curtin University is a trademark of Curtin University of Technology. CRICOS Provider Code 00301J (WA), 02637B (NSW)
___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
