Hi Peter,

OK, I've worked out why the terminal did not start up galaxy. I have done
that, performed a blastp search, and it failed with the usual error, but
now I have the terminal output for that failure.
Firstly the error report from galaxy:
----------------------------------------------------------------------
An error occurred running this job: blastp: 2.2.26+
Package: blast 2.2.26, build Aug 15 2012 17:48:54
BLAST Database error: No alias or index file found for protein database
[/media/sf_mikeds_bioinf/haldb/HAL_collection] in search path
[/var/lib/galaxy-server/database/job_working_directory/
----------------------------------------------------------------------


Now, the log output in the terminal window for that galaxy session: (DEBUG
flags are at the end)
----------------------------------------------------------------------------
127.0.0.1 - - [01/May/2013:20:49:58 +1100] "POST /root/user_get_usage
HTTP/1.1" 200 - "http://127.0.0.1:8080/history"; "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0"
galaxy.jobs.manager DEBUG 2013-05-01 20:49:59,237 (23) Job assigned to
handler 'main'
127.0.0.1 - - [01/May/2013:20:50:02 +1100] "POST /root/history_item_updates
HTTP/1.1" 200 - "http://127.0.0.1:8080/history"; "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0"
galaxy.jobs DEBUG 2013-05-01 20:50:04,403 (23) Working directory for job
is: /usr/lib/galaxy-server/database/job_working_directory/000/23
galaxy.jobs.handler DEBUG 2013-05-01 20:50:04,404 dispatching job 23 to
local runner
galaxy.jobs.handler INFO 2013-05-01 20:50:04,523 (23) Job dispatched
galaxy.jobs.runners.local DEBUG 2013-05-01 20:50:04,727 executing: python
/usr/lib/galaxy-server/tools/data_source/upload.py /usr/lib/galaxy-server
/usr/lib/galaxy-server/database/tmp/tmpckvivx
/usr/lib/galaxy-server/database/tmp/tmpED2TiJ
23:/usr/lib/galaxy-server/database/job_working_directory/000/23/dataset_23_files:/usr/lib/galaxy-server/database/files/000/dataset_23.dat
galaxy.jobs.runners.local DEBUG 2013-05-01 20:50:05,459 execution finished:
python /usr/lib/galaxy-server/tools/data_source/upload.py
/usr/lib/galaxy-server /usr/lib/galaxy-server/database/tmp/tmpckvivx
/usr/lib/galaxy-server/database/tmp/tmpED2TiJ
23:/usr/lib/galaxy-server/database/job_working_directory/000/23/dataset_23_files:/usr/lib/galaxy-server/database/files/000/dataset_23.dat
galaxy.jobs.runners.local DEBUG 2013-05-01 20:50:05,592 executing external
set_meta script for job 23: /usr/lib/galaxy-server/set_metadata.sh
./database/files
/usr/lib/galaxy-server/database/job_working_directory/000/23 .
/usr/lib/galaxy-server/universe_wsgi.ini
/usr/lib/galaxy-server/database/tmp/tmpckvivx
/usr/lib/galaxy-server/database/job_working_directory/000/23/galaxy.json
/usr/lib/galaxy-server/database/job_working_directory/000/23/metadata_in_HistoryDatasetAssociation_23_mZBOP0,/usr/lib/galaxy-server/database/job_working_directory/000/23/metadata_kwds_HistoryDatasetAssociation_23_ogpRq8,/usr/lib/galaxy-server/database/job_working_directory/000/23/metadata_out_HistoryDatasetAssociation_23_3yS7Yh,/usr/lib/galaxy-server/database/job_working_directory/000/23/metadata_results_HistoryDatasetAssociation_23_71mkqj,,/usr/lib/galaxy-server/database/job_working_directory/000/23/metadata_override_HistoryDatasetAssociation_23_KhG0tM
galaxy.jobs.runners.local DEBUG 2013-05-01 20:50:06,549 execution of
external set_meta for job 23 finished
galaxy.jobs DEBUG 2013-05-01 20:50:06,626 The tool did not define exit code
or stdio handling; checking stderr for success
127.0.0.1 - - [01/May/2013:20:50:06 +1100] "POST /root/history_item_updates
HTTP/1.1" 200 - "http://127.0.0.1:8080/history"; "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0"
galaxy.datatypes.metadata DEBUG 2013-05-01 20:50:06,773 loading metadata
from file for: HistoryDatasetAssociation 23
galaxy.jobs DEBUG 2013-05-01 20:50:06,905 job 23 ended
galaxy.datatypes.metadata DEBUG 2013-05-01 20:50:06,905 Cleaning up
external metadata files
127.0.0.1 - - [01/May/2013:20:50:10 +1100] "POST /root/history_item_updates
HTTP/1.1" 200 - "http://127.0.0.1:8080/history"; "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0"
127.0.0.1 - - [01/May/2013:20:50:10 +1100] "POST
/root/history_get_disk_size HTTP/1.1" 200 - "http://127.0.0.1:8080/history";
"Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:20.0) Gecko/20100101
Firefox/20.0"
127.0.0.1 - - [01/May/2013:20:50:11 +1100] "GET
/datasets/f09437b8822035f7/display/?preview=True HTTP/1.1" 200 - "
http://127.0.0.1:8080/history"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:20.0) Gecko/20100101 Firefox/20.0"
127.0.0.1 - - [01/May/2013:20:50:23 +1100] "GET
/tool_runner?tool_id=ncbi_blastp_wrapper HTTP/1.1" 200 - "
http://127.0.0.1:8080/root/tool_menu"; "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:20.0) Gecko/20100101 Firefox/20.0"
127.0.0.1 - - [01/May/2013:20:50:36 +1100] "POST /tool_runner/index
HTTP/1.1" 200 - "
http://127.0.0.1:8080/tool_runner?tool_id=ncbi_blastp_wrapper"; "Mozilla/5.0
(X11; Ubuntu; Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0"
127.0.0.1 - - [01/May/2013:20:50:37 +1100] "GET /history HTTP/1.1" 200 - "
http://127.0.0.1:8080/tool_runner/index"; "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:20.0) Gecko/20100101 Firefox/20.0"
127.0.0.1 - - [01/May/2013:20:50:37 +1100] "POST /root/user_get_usage
HTTP/1.1" 200 - "http://127.0.0.1:8080/history"; "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0"
127.0.0.1 - - [01/May/2013:20:50:41 +1100] "POST /root/history_item_updates
HTTP/1.1" 200 - "http://127.0.0.1:8080/history"; "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0"
galaxy.jobs.manager DEBUG 2013-05-01 20:50:41,334 (24) Job assigned to
handler 'main'
127.0.0.1 - - [01/May/2013:20:50:45 +1100] "POST /root/history_item_updates
HTTP/1.1" 200 - "http://127.0.0.1:8080/history"; "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0"
galaxy.jobs DEBUG 2013-05-01 20:50:46,447 (24) Working directory for job
is: /usr/lib/galaxy-server/database/job_working_directory/000/24
galaxy.jobs.handler DEBUG 2013-05-01 20:50:46,447 dispatching job 24 to
local runner
galaxy.jobs.handler INFO 2013-05-01 20:50:46,580 (24) Job dispatched
galaxy.jobs.runners.local DEBUG 2013-05-01 20:50:46,772 executing: blastp
-version &> /usr/lib/galaxy-server/database/tmp/GALAXY_VERSION_STRING_24;
python /usr/lib/galaxy-server/tools/ncbi_blast_plus/hide_stderr.py blastp
-query "/usr/lib/galaxy-server/database/files/000/dataset_23.dat"   -db
"/media/sf_mikeds_bioinf/haldb/HAL_collection" -task blastp -evalue 0.001
-out /usr/lib/galaxy-server/database/files/000/dataset_24.dat     -outfmt 6
-num_threads 8
127.0.0.1 - - [01/May/2013:20:50:49 +1100] "POST /root/history_item_updates
HTTP/1.1" 200 - "http://127.0.0.1:8080/history"; "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0"
galaxy.jobs.runners.local DEBUG 2013-05-01 20:50:49,568 execution finished:
blastp -version &>
/usr/lib/galaxy-server/database/tmp/GALAXY_VERSION_STRING_24; python
/usr/lib/galaxy-server/tools/ncbi_blast_plus/hide_stderr.py blastp -query
"/usr/lib/galaxy-server/database/files/000/dataset_23.dat"   -db
"/media/sf_mikeds_bioinf/haldb/HAL_collection" -task blastp -evalue 0.001
-out /usr/lib/galaxy-server/database/files/000/dataset_24.dat     -outfmt 6
-num_threads 8
galaxy.jobs.runners.local DEBUG 2013-05-01 20:50:49,658 executing external
set_meta script for job 24: /usr/lib/galaxy-server/set_metadata.sh
./database/files
/usr/lib/galaxy-server/database/job_working_directory/000/24 .
/usr/lib/galaxy-server/universe_wsgi.ini
/usr/lib/galaxy-server/database/tmp/tmpckvivx
/usr/lib/galaxy-server/database/job_working_directory/000/24/galaxy.json
/usr/lib/galaxy-server/database/job_working_directory/000/24/metadata_in_HistoryDatasetAssociation_24_Z7Rv70,/usr/lib/galaxy-server/database/job_working_directory/000/24/metadata_kwds_HistoryDatasetAssociation_24_NGaXc0,/usr/lib/galaxy-server/database/job_working_directory/000/24/metadata_out_HistoryDatasetAssociation_24_0FT0mx,/usr/lib/galaxy-server/database/job_working_directory/000/24/metadata_results_HistoryDatasetAssociation_24_U1RFk9,,/usr/lib/galaxy-server/database/job_working_directory/000/24/metadata_override_HistoryDatasetAssociation_24_PI3NHu
galaxy.jobs.runners.local DEBUG 2013-05-01 20:50:50,616 execution of
external set_meta for job 24 finished
galaxy.jobs DEBUG 2013-05-01 20:50:50,635 The tool did not define exit code
or stdio handling; checking stderr for success
galaxy.jobs DEBUG 2013-05-01 20:50:50,686 setting dataset state to ERROR
galaxy.jobs DEBUG 2013-05-01 20:50:50,817 job 24 ended
galaxy.datatypes.metadata DEBUG 2013-05-01 20:50:50,817 Cleaning up
external metadata files
127.0.0.1 - - [01/May/2013:20:50:53 +1100] "POST /root/history_item_updates
HTTP/1.1" 200 - "http://127.0.0.1:8080/history"; "Mozilla/5.0 (X11; Ubuntu;
Linux x86_64; rv:20.0) Gecko/20100101 Firefox/20.0"
127.0.0.1 - - [01/May/2013:20:50:53 +1100] "POST
/root/history_get_disk_size HTTP/1.1" 200 - "http://127.0.0.1:8080/history";
"Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:20.0) Gecko/20100101
Firefox/20.0"
------------------------------------------------------------------------------


Regards, Mike





On Wed, May 1, 2013 at 8:43 PM, Mike Dyall-Smith
<mike.dyallsm...@gmail.com>wrote:

> Hi Peter,
>
> In biolinux, I start galaxy by a clicking on an application icon.
>
> If I open the terminal and run the suggested command: $ sh run.sh | grep
> -i blast
> I get the following output (long):
>
> $ sudo sh run.sh | grep -i blast
> python path is:
> /usr/lib/galaxy-server/eggs/numpy-1.6.0-py2.7-linux-x86_64-ucs4.egg,
> /usr/lib/galaxy-server/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg,
> /usr/lib/galaxy-server/eggs/boto-2.2.2-py2.7.egg,
> /usr/lib/galaxy-server/eggs/mercurial-2.1.2-py2.7-linux-x86_64-ucs4.egg,
> /usr/lib/galaxy-server/eggs/Fabric-1.4.2-py2.7.egg,
> /usr/lib/galaxy-server/eggs/ssh-1.7.14-py2.7.egg,
> /usr/lib/galaxy-server/eggs/Whoosh-0.3.18-py2.7.egg,
> /usr/lib/galaxy-server/eggs/pycrypto-2.5-py2.7-linux-x86_64-ucs4.egg,
> /usr/lib/galaxy-server/eggs/python_lzo-1.08_2.03_static-py2.7-linux-x86_64-ucs4.egg,
> /usr/lib/galaxy-server/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-x86_64-ucs4.egg,
> /usr/lib/galaxy-server/eggs/amqplib-0.6.1-py2.7.egg,
> /usr/lib/galaxy-server/eggs/pexpect-2.4-py2.7.egg,
> /usr/lib/galaxy-server/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.7.egg,
> /usr/lib/galaxy-server/eggs/Babel-0.9.4-py2.7.egg,
> /usr/lib/galaxy-server/eggs/Mako-0.4.1-py2.7.egg,
> /usr/lib/galaxy-server/eggs/WebHelpers-0.2-py2.7.egg,
> /usr/lib/galaxy-server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs4.egg,
> /usr/lib/galaxy-server/eggs/wchartype-0.1-py2.7.egg,
> /usr/lib/galaxy-server/eggs/elementtree-1.2.6_20050316-py2.7.egg,
> /usr/lib/galaxy-server/eggs/docutils-0.7-py2.7.egg,
> /usr/lib/galaxy-server/eggs/WebOb-0.8.5-py2.7.egg,
> /usr/lib/galaxy-server/eggs/Routes-1.12.3-py2.7.egg,
> /usr/lib/galaxy-server/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg,
> /usr/lib/galaxy-server/eggs/PasteDeploy-1.3.3-py2.7.egg,
> /usr/lib/galaxy-server/eggs/PasteScript-1.7.3-py2.7.egg,
> /usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg,
> /usr/lib/galaxy-server/lib, /usr/lib/python2.7,
> /usr/lib/python2.7/plat-linux2, /usr/lib/python2.7/lib-tk,
> /usr/lib/python2.7/lib-old, /usr/lib/python2.7/lib-dynload,
> /usr/local/lib/python2.7/dist-packages,
> /usr/lib/python2.7/dist-packages/PIL,
> /usr/lib/python2.7/dist-packages/gst-0.10,
> /usr/lib/python2.7/dist-packages/gtk-2.0, /usr/lib/pymodules/python2.7,
> /usr/lib/python2.7/dist-packages/ubuntu-sso-client,
> /usr/lib/python2.7/dist-packages
> galaxy.datatypes.registry DEBUG 2013-05-01 19:58:26,358 Loaded sniffer for
> datatype 'galaxy.datatypes.xml:BlastXml'
> galaxy.tools.data DEBUG 2013-05-01 19:58:26,371 Loaded tool data table
> 'blastdb'
> galaxy.tools.data DEBUG 2013-05-01 19:58:26,372 Loaded tool data table
> 'blastdb_p'
> galaxy.tools DEBUG 2013-05-01 19:58:30,808 Loading section: NCBI BLAST+
> galaxy.tools DEBUG 2013-05-01 19:58:30,808 Loaded tool id:
> ncbi_blastn_wrapper, version: 0.0.11.
> galaxy.tools DEBUG 2013-05-01 19:58:30,808 Loaded tool id:
> ncbi_blastp_wrapper, version: 0.0.11.
> galaxy.tools DEBUG 2013-05-01 19:58:30,809 Loaded tool id:
> ncbi_blastx_wrapper, version: 0.0.11.
> galaxy.tools DEBUG 2013-05-01 19:58:30,809 Loaded tool id:
> ncbi_tblastn_wrapper, version: 0.0.11.
> galaxy.tools DEBUG 2013-05-01 19:58:30,809 Loaded tool id:
> ncbi_tblastx_wrapper, version: 0.0.11.
> galaxy.tools DEBUG 2013-05-01 19:58:30,809 Loaded tool id:
> blastxml_to_tabular, version: 0.0.8.
> galaxy.tools DEBUG 2013-05-01 19:58:30,813 Loaded tool id:
> megablast_wrapper, version: 1.2.0.
> galaxy.tools DEBUG 2013-05-01 19:58:30,813 Loaded tool id:
> megablast_xml_parser, version: 1.0.0.
> Traceback (most recent call last):
>   File "./scripts/paster.py", line 34, in <module>
>     command.run()
>   File
> "/usr/lib/galaxy-server/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
> line 84, in run
>     invoke(command, command_name, options, args[1:])
>   File
> "/usr/lib/galaxy-server/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
> line 123, in invoke
>     exit_code = runner.run(args)
>   File
> "/usr/lib/galaxy-server/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
> line 218, in run
>     result = self.command()
>   File
> "/usr/lib/galaxy-server/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py",
> line 303, in command
>     serve()
>   File
> "/usr/lib/galaxy-server/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py",
> line 287, in serve
>     server(app)
>   File
> "/usr/lib/galaxy-server/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
> line 151, in server_wrapper
>     **context.local_conf)
>   File
> "/usr/lib/galaxy-server/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/util/fixtypeerror.py",
> line 57, in fix_call
>     val = callable(*args, **kw)
>   File
> "/usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line
> 1314, in server_runner
>     serve(wsgi_app, **kwargs)
>   File
> "/usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line
> 1264, in serve
>     threadpool_options=threadpool_options)
>   File
> "/usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line
> 1114, in __init__
>     RequestHandlerClass, ssl_context)
>   File
> "/usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line
> 1094, in __init__
>     RequestHandlerClass, ssl_context)
>   File
> "/usr/lib/galaxy-server/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line
> 358, in __init__
>     HTTPServer.__init__(self, server_address, RequestHandlerClass)
>   File "/usr/lib/python2.7/SocketServer.py", line 408, in __init__
>     self.server_bind()
>   File "/usr/lib/python2.7/BaseHTTPServer.py", line 108, in server_bind
>     SocketServer.TCPServer.server_bind(self)
>   File "/usr/lib/python2.7/SocketServer.py", line 419, in server_bind
>     self.socket.bind(self.server_address)
>   File "/usr/lib/python2.7/socket.py", line 224, in meth
>     return getattr(self._sock,name)(*args)
> socket.error: [Errno 98] Address already in use
>
> ----------------------------------------------------------------------------------------------
> as might be expected from this output, it doesn't start up galaxy at
> localhost.
>
>
> >check is the read permissions on the BLAST database
>   Well, from the terminal, I have access to all those files. The
> permissions are all the same, e.g.
>    -rwxrwx--- 1      root       vboxsf   15721925 Apr 10 18:55
> nr.00.phd
>
>  Within galaxy, I can open them with the get data menu command.
>
> >... Galaxy log output
> How is the best way to get that?
>
> In other news, I was able to get galaxy working on the host OS X system.
> This took a long time, but finally, within virtualenv, and with many
> repeated attempts to get all the python egg dependencies, I got it up and
> running. In the process, I seem to have deleted some of the old python
> files in the OS X system (trying to force it to use the macports py27
> installation). Perhaps the OS X instance will be OK but it does not come
> with the blast tools that I want, and I do not see an easy way to install
> them (I don't see an admin button to automatically install them).
>
> Now that I've played with linux, I can see that it is not so bad to use.
> Apple seems to have dropped the ball with facilitating scientific
> computing. From your advice, it seems that instead of spending any more of
> my time trying to set up galaxy on my laptop, I should look around for ssh
> access to an existing galaxy server.
>
> Regards, Mike DS
>
>
>
>
>
>
> On Wed, May 1, 2013 at 7:26 PM, Peter Cock <p.j.a.c...@googlemail.com>wrote:
>
>> Hi Mike,
>>
>> On Tue, Apr 30, 2013 at 11:17 PM, Mike Dyall-Smith
>> <mike.dyallsm...@gmail.com> wrote:
>> > Thanks Peter. My answers are below:
>> >
>> >>What query sequences are you using?
>> > I have just been using one fasta protein sequence.
>>
>> OK - this and the fact it works on the host machine is good to know.
>>
>> >>Meanwhile monitor the system with top
>> > Top says only a max of 27% cpu usage, but the linux screen eventually
>> > freezes, and I have to restart. I am not sure how to read out RAM and
>> disk
>> > IO from top.
>>
>> Linux 'top' does list memory usage, both per process and for
>> the system in the text at the top. There are other tools for
>> monitoring IO like iotop - but you could also probably just
>> watch the host Apple OS X System Monitor for this.
>>
>> This does sound like the VM hasn't got enough RAM to run
>> BLASTP against NR efficiently.
>>
>> >>grep blastp paster.log
>> > Tried that, and it says there is no such file or directory
>>
>> In the Galaxy folder? Maybe the default log filename has
>> changed since I setup my machine... are you running Galaxy
>> as a daemon, or running run.sh at the terminal directly? If the
>> later, try something like this:
>>
>> $ sh run.sh | grep -i blast
>>
>> (If you don't get much output, adjust the logging level in the
>> universe_wgsi.ini configuration file.)
>>
>> >>Could you try running BLAST from the host Mac OX
>> > Yes. And it works fine! I get a good match in a relatively short time.
>>
>> That's progress - the hardware itself is capable :)
>>
>> > I then made a very small protein database, checked it by commandline
>> blastp
>> > in both host OS X and in guest linux, and it worked fine. Added it to
>> the
>> > blastdb_p.loc file, restarted and saw it listed in galaxy. Tried to use
>> it
>> > for a blastp, and got the same error as before with the huge NCBI nr
>> > database. So, it is not a matter of size....
>>
>> There are clearly two separate issues, (1) getting BLAST to run nicely
>> on your VM - which I think is running out of RAM, and (2) sorting out
>> your Galaxy BLAST database configuration.
>>
>> Something to check is the read permissions on the BLAST database
>> files (which Linux user are you running Galaxy as, and can that user
>> read the database files and their folder?).
>>
>> I'm keen to see the Galaxy log output to see what exactly was the
>> command line being used to run BLAST, which would help with
>> debugging where the problem is.
>>
>> > Thanks for your comments about RAM and blast searches. It gives me hope
>> that
>> > I can get galaxy running usefully.  I only chose biolinux because of the
>> > suite of programs and the apparent ease of use. The other reason was
>> that I
>> > could not install galaxy on OS X (10.6). I get errors that others have
>> noted
>> > on the discussion lists but no-one seems to have a solution for.
>>
>> I used to do my Galaxy tool development on Mac OS X, but it didn't
>> work 100% right, and in any case many of the tools I wanted to
>> wrap and run within Galaxy were Linux only - so now I just ssh
>> into a Linux server to do Galaxy work. Given the main Galaxy
>> development and the Penn state Galaxy server all happens on
>> Linux, you'll have a much easier time under Linux than Mac OS X.
>>
>> Regards,
>>
>> Peter
>>
>
>
>
> --
> _____________________________________
> Mike Dyall-Smith, Ph.D.,
>
>
>
>
>



-- 
_____________________________________
Mike Dyall-Smith, Ph.D.,
Charles Sturt University,
PO Box U183,
Wagga Wagga
Australia  2678

Tel: +61 (0)2 693 32029
email: mike.dyallsm...@gmail.com
web: www.haloarchaea.com
skype: mike.dyallsmith
_____________________________________

On measuring microbial diversity:

"This is like randomly sampling a bus load of people and then trying to
infer the diversity of all people in the world. You would not expect to
find many Lithuanians." - Curtis and Sloan, 2005
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