Hi Eleanora, I am glad the update worked. Please keep the mailing list thread alive by using "reply all". You are missing many smart people thinking about your problem if you don't. :)
Let us know how it goes. Martin On Wed, May 20, 2015, 02:52 Eleanor Morgan <e.mor...@curtin.edu.au> wrote: > Hi Martin, > > Apologies. Ignore this message. I needed to update the database, I > expected the script would tell me this up front, but I found the message in > paster.log (which I should have checked first). I’ll get back to you on my > progress with Tophat etc. > > 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 > Web | biomed.curtin.edu.au > > > > 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> > Date: Wednesday, 20 May 2015 1:44 pm > To: Martin Čech <mar...@bx.psu.edu> > > Subject: Re: [galaxy-dev] tophat2 failing to execute > > Hello Martin, > > Thank you very much for your reply and suggestions. I removed the > /static/scripts/packed folder and reran the update. This time I got > through the process. However, I cannot seem to get galaxy to start up. > As the root user I initiated startup from the init.d/galaxy script > > /etc/init.d/galaxy start > Starting galaxy... > Initializing config/migrated_tools_conf.xml from > migrated_tools_conf.xml.sample > Initializing config/shed_tool_conf.xml from shed_tool_conf.xml.sample > Initializing config/shed_tool_data_table_conf.xml from > shed_tool_data_table_conf.xml.sample > Initializing config/shed_data_manager_conf.xml from > shed_data_manager_conf.xml.sample > Some eggs are out of date, attempting to fetch... > Fetched http://eggs.galaxyproject.org/repoze.lru/repoze.lru-0.6-py2.6.egg > Fetched http://eggs.galaxyproject.org/Whoosh/Whoosh-2.4.1-py2.6.egg > Removed conflicting egg: /galaxy/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg > Fetched http://eggs.galaxyproject.org/sqlparse/sqlparse-0.1.14-py2.6.egg > Fetched http://eggs.galaxyproject.org/amqp/amqp-1.4.6-py2.6.egg > Removed conflicting egg: /galaxy/galaxy-dist/eggs/amqp-1.4.3-py2.6.egg > Fetched http://eggs.galaxyproject.org/bioblend/bioblend-0.5.2-py2.6.egg > Removed conflicting egg: /galaxy/galaxy-dist/eggs/bioblend-0.4.2-py2.6.egg > Fetched http://eggs.galaxyproject.org/kombu/kombu-3.0.24-py2.6.egg > Removed conflicting egg: /galaxy/galaxy-dist/eggs/kombu-3.0.12-py2.6.egg > Fetched > http://eggs.galaxyproject.org/SQLAlchemy/SQLAlchemy-1.0.1-py2.6-linux-x86_64-ucs4.egg > Removed conflicting egg: > /galaxy/galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs4.egg > Fetched http://eggs.galaxyproject.org/Routes/Routes-2.1-py2.6.egg > Removed conflicting egg: /galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg > Fetched http://eggs.galaxyproject.org/six/six-1.9.0-py2.6.egg > Fetched > http://eggs.galaxyproject.org/mercurial/mercurial-3.2.4-py2.6-linux-x86_64-ucs4.egg > Removed conflicting egg: > /galaxy/galaxy-dist/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg > sqlalchemy_migrate 0.9.6 couldn't be downloaded automatically. You can try > building it by hand with: > python scripts/scramble.py -c universe_wsgi.ini -e sqlalchemy_migrate > Fetch failed. > Entering daemon mode > ...done. > > > There appears to be an error since I see Fetch failed. But there is no > message telling me galaxy failed to start. However, there is no evidence > that it is running when I check processes, and the website is not up. > > > I then try stopping and starting > > > [root@binfmt01:/home/175146F]# /etc/init.d/galaxy stop > > Stopping galaxy... No PID file exists in paster.pid > > done. > > [root@binfmt01:/home/175146F]# /etc/init.d/galaxy start > > Starting galaxy... > > Entering daemon mode > > …done. > > > Again, there is no evidence that it is not starting. The web service > does not start up, however and if I check the status I get this: > > /etc/init.d/galaxy status > > galaxy status: stopped > > > Any suggestions on how I can get around this problem will be greatly > appreciated. > > > Regards, > > Eleanor > > > > From: Martin Čech <mar...@bx.psu.edu> > Date: Wednesday, 20 May 2015 11:52 am > To: Eleanor Morgan <e.mor...@curtin.edu.au>, "galaxy-...@lists.bx.psu.edu" > <galaxy-...@lists.bx.psu.edu> > Subject: Re: [galaxy-dev] tophat2 failing to execute > > Hello Eleanor, > > it seems there are multiple issues present. > > First of all in the 15.05 release the static/scripts/packed folder has > been changed to a symlink aiming at static/scripts (this is a part of > internal scriptbuild transition). If it is not a symlink in your filesystem > you can safely remove that folder (static/scripts/packed) with its contents > and update again to receive the correct symlink. That should help you with > the merging of the update. > > Once updated (and please let us know if more trouble arise) we can start > troubleshooting why you canot connect to the Tool Shed (TS). Are you trying > to 'Search and browse tool sheds' in the Admin menu? What is your Galaxy > setup? Are you behind any proxy? What changed since the point at which you > were able to reach TS? > > When it comes to the tophat2 error: the log that can tell you more is > (by default) printed in the console window in which you run Galaxy. If > tophat fails you should see some exceptions or at least a more explicit > error there. > > As a side note it is good to know that the tophat you have locally > installed on your machine is probably not the tophat Galaxy is using while > running the tophat tool. Galaxy will try to use the TS tophat dependency > installed from the package_tophat2_2_0_9. > > Please let us know how it goes. > > Thank you > > Martin, Galaxy Team > > > On Tue, May 19, 2015 at 11:28 PM Eleanor Morgan <e.mor...@curtin.edu.au> > wrote: > >> 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 >> Web | biomed.curtin.edu.au >> >> >> >> 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> >> Date: Tuesday, 19 May 2015 9:50 pm >> To: "galaxy-...@lists.bx.psu.edu" <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 >> Web | biomed.curtin.edu.au >> >> >> >> 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/ > >
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