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.Morgan@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.morgan@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.morgan@curtin.edu.au> Date: Wednesday, 20 May 2015 1:44 pm To: Martin Čech <marten@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Initializing config/shed_data_manager_conf.xml from shed_data_manager_conf.xml.sample Some eggs are out of date, attempting to fetch...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... 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-u... 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 <marten@bx.psu.edu> Date: Wednesday, 20 May 2015 11:52 am To: Eleanor Morgan <e.morgan@curtin.edu.au>, "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@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.Morgan@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.morgan@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.morgan@curtin.edu.au> Date: Tuesday, 19 May 2015 9:50 pm To: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@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.morgan@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)

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