Re: [galaxy-dev] Installing Galaxy on Freebsd 10.0

[ashish damania]

Just a hunch, do you guys think  pysam is the cause of these issues?
From: ashis...@hotmail.com
To: dannon.ba...@gmail.com
CC: galaxy-dev@lists.bx.psu.edu
Subject: RE: [galaxy-dev] Installing Galaxy on Freebsd 10.0
Date: Wed, 10 Sep 2014 19:21:33 -0500




Hi Dannon,
Thanks for the reply. 
##
 python --version








Python 2.7.3# cd galaxy-dist*# rm -rf eggs#python scripts/fetch_eggs.py
/*Running this command after deleting egg folder */ 








Fetched http://eggs.galaxyproject.org/docutils/docutils-0.7-py2.7.egg
Fetched http://eggs.galaxyproject.org/kombu/kombu-3.0.13-py2.7.egg
Fetched http://eggs.galaxyproject.org/mock/mock-1.0.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/raven/raven-3.1.8-py2.7.egg
Fetched http://eggs.galaxyproject.org/Beaker/Beaker-1.4-py2.7.egg
Traceback (most recent call last):
  File "scripts/fetch_eggs.py", line 37, in 
c.resolve() # Only fetch eggs required by the config
  File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, 
in resolve
egg.resolve()
  File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, 
in resolve
return self.version_conflict( e.args[0], e.args[1] )
  File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, 
in version_conflict
r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, 
egg.fetch )
  File "/usr/home/ec2-user/galaxy-dist/lib/pkg_resources.py", line 565, in 
resolve
raise DistributionNotFound(req)  # XXX put more info here
pkg_resources.DistributionNotFound: PyYAML==3.10
==

I ran the command again without deleting the "egg" folder and this is what I 
got 
==#python
 scripts/fetch_eggs.py /*Running this command 2nd time  without deleting 
egg folder */








Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Warning: pycrypto (a dependent egg of Fabric) cannot be fetched
Warning: pytz (a dependent egg of Babel) cannot be fetched
Fetched http://eggs.galaxyproject.org/paramiko/paramiko-1.11.1-py2.7.egg
One of Galaxy's managed eggs depends on something which is missing, this is 
almost certainly a bug in the egg distribution.
Dependency "paramiko" requires "pycrypto>=2.1,!=2.4"
Traceback (most recent call last):
  File "scripts/fetch_eggs.py", line 37, in 
c.resolve() # Only fetch eggs required by the config
  File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, 
in resolve
egg.resolve()
  File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/eggs/__init__.py", line 168, 
in resolve
dists = pkg_resources.working_set.resolve( ( 
self.distribution.as_requirement(), ), env, self.fetch )
  File "/usr/home/ec2-user/galaxy-dist/lib/pkg_resources.py", line 569, in 
resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (paramiko 1.11.1 
(/usr/home/ec2-user/galaxy-dist/eggs/paramiko-1.11.1-py2.7.egg), 
Requirement.parse('pycrypto>=2.1,!=2.4'))=====
Can you think of any other reasons? It works well on OS X and Ubuntu. 

-Ashish


Date: Wed, 10 Sep 2014 16:59:13 -0400
Subject: Re: [galaxy-dev] Installing Galaxy on Freebsd 10.0
From: dannon.ba...@gmail.com
To: ashis...@hotmail.com
CC: galaxy-dev@lists.bx.psu.edu

Hey Ashish,
We have an open issue to sort out exactly why/how this happens, but a quick fix 
for many users is just to remove your eggs/ folder and all eggs and re-run 
`python scripts/fetch_eggs.py`.  Give that a shot, but do let me know if it 
doesn't' work.

On Wed, Sep 10, 2014 at 4:54 PM, ashish damania  wrote:



# sh run.shSome eggs are out of date, attempting to fetch...Warning: setuptools 
(a dependent egg of sqlalchemy-migrate) cannot be fetchedWarning: simplejson (a 
dependent egg of bioblend) cannot be fetchedsimplejson 2.1.1 couldn't be 
downloaded automatically. You can trybuilding it by hand with: python 
scripts/scramble.py -e simplejsonFetch failed.Traceback (most recent call 
last): File 
"/usr/home/ec2-user/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 
38, in app_factory from galaxy.app import UniverseApplication File 
"/usr/home/ec2-user/galaxy-dist/lib/galaxy/app.py", line 12, in  from 
galaxy.visualization.data_providers.registry import DataProviderRegistry File 
"/usr/home/ec2-user/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py",
 line 2, in  from galaxy.visualization.data_providers import genome 
Fil

Re: [galaxy-dev] Installing Galaxy on Freebsd 10.0

[ashish damania]

Hi Dannon,
Thanks for the reply. 
##
 python --version








Python 2.7.3# cd galaxy-dist*# rm -rf eggs#python scripts/fetch_eggs.py
/*Running this command after deleting egg folder */ 








Fetched http://eggs.galaxyproject.org/docutils/docutils-0.7-py2.7.egg
Fetched http://eggs.galaxyproject.org/kombu/kombu-3.0.13-py2.7.egg
Fetched http://eggs.galaxyproject.org/mock/mock-1.0.1-py2.7.egg
Fetched http://eggs.galaxyproject.org/raven/raven-3.1.8-py2.7.egg
Fetched http://eggs.galaxyproject.org/Beaker/Beaker-1.4-py2.7.egg
Traceback (most recent call last):
  File "scripts/fetch_eggs.py", line 37, in 
c.resolve() # Only fetch eggs required by the config
  File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, 
in resolve
egg.resolve()
  File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/eggs/__init__.py", line 195, 
in resolve
return self.version_conflict( e.args[0], e.args[1] )
  File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/eggs/__init__.py", line 226, 
in version_conflict
r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, 
egg.fetch )
  File "/usr/home/ec2-user/galaxy-dist/lib/pkg_resources.py", line 565, in 
resolve
raise DistributionNotFound(req)  # XXX put more info here
pkg_resources.DistributionNotFound: PyYAML==3.10
==

I ran the command again without deleting the "egg" folder and this is what I 
got 
==#python
 scripts/fetch_eggs.py /*Running this command 2nd time  without deleting 
egg folder */








Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Warning: pycrypto (a dependent egg of Fabric) cannot be fetched
Warning: pytz (a dependent egg of Babel) cannot be fetched
Fetched http://eggs.galaxyproject.org/paramiko/paramiko-1.11.1-py2.7.egg
One of Galaxy's managed eggs depends on something which is missing, this is 
almost certainly a bug in the egg distribution.
Dependency "paramiko" requires "pycrypto>=2.1,!=2.4"
Traceback (most recent call last):
  File "scripts/fetch_eggs.py", line 37, in 
c.resolve() # Only fetch eggs required by the config
  File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, 
in resolve
egg.resolve()
  File "/usr/home/ec2-user/galaxy-dist/lib/galaxy/eggs/__init__.py", line 168, 
in resolve
dists = pkg_resources.working_set.resolve( ( 
self.distribution.as_requirement(), ), env, self.fetch )
  File "/usr/home/ec2-user/galaxy-dist/lib/pkg_resources.py", line 569, in 
resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (paramiko 1.11.1 
(/usr/home/ec2-user/galaxy-dist/eggs/paramiko-1.11.1-py2.7.egg), 
Requirement.parse('pycrypto>=2.1,!=2.4'))=====
Can you think of any other reasons? It works well on OS X and Ubuntu. 

-Ashish


Date: Wed, 10 Sep 2014 16:59:13 -0400
Subject: Re: [galaxy-dev] Installing Galaxy on Freebsd 10.0
From: dannon.ba...@gmail.com
To: ashis...@hotmail.com
CC: galaxy-dev@lists.bx.psu.edu

Hey Ashish,
We have an open issue to sort out exactly why/how this happens, but a quick fix 
for many users is just to remove your eggs/ folder and all eggs and re-run 
`python scripts/fetch_eggs.py`.  Give that a shot, but do let me know if it 
doesn't' work.

On Wed, Sep 10, 2014 at 4:54 PM, ashish damania  wrote:



# sh run.shSome eggs are out of date, attempting to fetch...Warning: setuptools 
(a dependent egg of sqlalchemy-migrate) cannot be fetchedWarning: simplejson (a 
dependent egg of bioblend) cannot be fetchedsimplejson 2.1.1 couldn't be 
downloaded automatically. You can trybuilding it by hand with: python 
scripts/scramble.py -e simplejsonFetch failed.Traceback (most recent call 
last): File 
"/usr/home/ec2-user/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 
38, in app_factory from galaxy.app import UniverseApplication File 
"/usr/home/ec2-user/galaxy-dist/lib/galaxy/app.py", line 12, in  from 
galaxy.visualization.data_providers.registry import DataProviderRegistry File 
"/usr/home/ec2-user/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py",
 line 2, in  from galaxy.visualization.data_providers import genome 
File 
"/usr/home/ec2-user/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py",
 line 17, in  from pysam import !csamtools, ctabix File 
"/usr/home/ec2-user/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-freebsd-10.0-RELEASE-p7-amd64-ucs

Re: [galaxy-dev] Installing Galaxy on Freebsd 10.0

[Dannon Baker]

Hey Ashish,

We have an open issue to sort out exactly why/how this happens, but a quick
fix for many users is just to remove your eggs/ folder and all eggs and
re-run `python scripts/fetch_eggs.py`.  Give that a shot, but do let me
know if it doesn't' work.


On Wed, Sep 10, 2014 at 4:54 PM, ashish damania 
wrote:

> # sh run.sh
> Some eggs are out of date, attempting to fetch...Warning: setuptools (a 
> dependent egg of sqlalchemy-migrate) cannot be fetchedWarning: simplejson (a 
> dependent egg of bioblend) cannot be fetchedsimplejson 2.1.1 couldn't be 
> downloaded automatically. You can trybuilding it by hand with: python 
> scripts/scramble.py -e simplejsonFetch failed.Traceback (most recent call 
> last): File 
> "/usr/home/ec2-user/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 
> 38, in app_factory from galaxy.app import UniverseApplication File 
> "/usr/home/ec2-user/galaxy-dist/lib/galaxy/app.py", line 12, in  from 
> galaxy.visualization.data_providers.registry import DataProviderRegistry File 
> "/usr/home/ec2-user/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py",
>  line 2, in  from galaxy.visualization.data_providers import genome 
> File 
> "/usr/home/ec2-user/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py",
>  line 17, in  from pysam import !
> csamtools, ctabix File 
> "/usr/home/ec2-user/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-freebsd-10.0-RELEASE-p7-amd64-ucs2.egg/pysam/__init__.py",
>  line 1, in  from csamtools import *ImportError: 
> /usr/home/ec2-user/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-freebsd-10.0-RELEASE-p7-amd64-ucs2.egg/csamtools.so:
>  Undefined symbol "__ks_insertsort_heap"
>
> So I have tried running this script
> python scripts/scramble.py -e simplejson
> ​
> Traceback (most recent call last): File "scripts/scramble.py", line 50, in 
>  egg.scramble() File 
> "/usr/home/ec2-user/galaxy-dist/lib/galaxy/eggs/scramble.py", line 60, in 
> scramble raise ScrambleFailure( self, "%s(): Egg build for %s did not appear 
> to fail, but no egg found to copy from expected path:\n %s" % ( 
> sys._getframe().f_code.co_name, self.name, new_egg ) 
> )galaxy.eggs.scramble.ScrambleFailure: scramble(): Egg build for simplejson 
> did not appear to fail, but no egg found to copy from expected path: 
> /usr/home/ec2-user/galaxy-dist/scripts/scramble/build/py2.7/simplejson/dist/simplejson-2.1.1-py2.7.egg
>
>
> I found that I have file named: 
> "simplejson-2.1.1-py2.7-freebsd-10.0-RELEASE-p7-amd64-ucs2.egg" in the 
> "../scripts/scramble/build/py2.7/simplejson/dist/" folder. I renamed that 
> file simplejson-2.1.1-py2.7.egg but it gives me that same error when I 
> execute "sh run.sh".
>
>
> Is it ok to run Galaxy under Freebsd 10.0? Are there any compatibility issues?
>
> Thanks you.
>
>
> ___
> 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:
>   http://lists.bx.psu.edu/
>
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>
___
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[galaxy-dev] Installing Galaxy on Freebsd 10.0

[ashish damania]

# sh run.shSome eggs are out of date, attempting to fetch...Warning: setuptools 
(a dependent egg of sqlalchemy-migrate) cannot be fetchedWarning: simplejson (a 
dependent egg of bioblend) cannot be fetchedsimplejson 2.1.1 couldn't be 
downloaded automatically. You can trybuilding it by hand with: python 
scripts/scramble.py -e simplejsonFetch failed.Traceback (most recent call 
last): File 
"/usr/home/ec2-user/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 
38, in app_factory from galaxy.app import UniverseApplication File 
"/usr/home/ec2-user/galaxy-dist/lib/galaxy/app.py", line 12, in  from 
galaxy.visualization.data_providers.registry import DataProviderRegistry File 
"/usr/home/ec2-user/galaxy-dist/lib/galaxy/visualization/data_providers/registry.py",
 line 2, in  from galaxy.visualization.data_providers import genome 
File 
"/usr/home/ec2-user/galaxy-dist/lib/galaxy/visualization/data_providers/genome.py",
 line 17, in  from pysam import !csamtools, ctabix File 
"/usr/home/ec2-user/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-freebsd-10.0-RELEASE-p7-amd64-ucs2.egg/pysam/__init__.py",
 line 1, in  from csamtools import *ImportError: 
/usr/home/ec2-user/galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-freebsd-10.0-RELEASE-p7-amd64-ucs2.egg/csamtools.so:
 Undefined symbol "__ks_insertsort_heap"So I have tried running this 
scriptpython scripts/scramble.py -e simplejson​Traceback (most recent call 
last): File "scripts/scramble.py", line 50, in  egg.scramble() File 
"/usr/home/ec2-user/galaxy-dist/lib/galaxy/eggs/scramble.py", line 60, in 
scramble raise ScrambleFailure( self, "%s(): Egg build for %s did not appear to 
fail, but no egg found to copy from expected path:\n %s" % ( 
sys._getframe().f_code.co_name, self.name, new_egg ) 
)galaxy.eggs.scramble.ScrambleFailure: scramble(): Egg build for simplejson did 
not appear to fail, but no egg found to copy from expected path: 
/usr/home/ec2-user/galaxy-dist/scripts/scramble/build/py2.7/simplejson/dist/simplejson-2.1.1-py2.7.eggI
 found that I have file named: 
"simplejson-2.1.1-py2.7-freebsd-10.0-RELEASE-p7-amd64-ucs2.egg" in the 
"../scripts/scramble/build/py2.7/simplejson/dist/" folder. I renamed that file 
simplejson-2.1.1-py2.7.egg but it gives me that same error when I execute "sh 
run.sh".Is it ok to run Galaxy under Freebsd 10.0? Are there any compatibility 
issues?Thanks you.___
Please keep all replies on the list by using "reply all"
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Re: [galaxy-dev] Installing galaxy with Apache

[Matthias Enders]

Hi John,

your solution perfectly solved my problem.

Thank you!

-Ursprüngliche Nachricht-
Von: John Chilton [mailto:jmchil...@gmail.com] 
Gesendet: Friday, June 06, 2014 3:32 PM
An: Matthias Enders
Cc: galaxy-...@bx.psu.edu
Betreff: Re: [galaxy-dev] Installing galaxy with Apache

Hmm... sorry for the delay I hope you got this to work. I feel like someone 
should respond to this but it is difficult to remotely debug web server 
configuration issues.

Should your apache config line:

RewriteRule ^(.*) http://localhost:8080$1 [P]

be:

RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]

instead?

That is the only guess I have. Thanks for your interest in deploying Galaxy.

-John


On Mon, Jun 2, 2014 at 7:37 AM, Matthias Enders 
 wrote:
> Hi,
>
>
>
> this thread is likely related to this one:
>
>
>
> http://user.list.galaxyproject.org/Installing-galaxy-with-Apache-td465
> 4499.html
>
>
>
> I installed Galaxy on a Ubuntu Server 12.04 system. I followed the 
> instruction on the link mentioned above and this one:
>
> https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
>
>
>
> Now my issue is:
>
>
>
> When I got this configuration in my /etc/apache2/sites-available/default :
>
>
>
> RewriteEngine on
>
> RewriteRule ^/galaxy$ /galaxy/ [R]
>
> RewriteRule ^/galaxy/static/style/(.*)
> /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
>
> RewriteRule ^/galaxy/static/scripts/(.*)
> /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L]
>
> RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 
> [L]
>
> RewriteRule ^/galaxy/favicon.ico 
> /home/galaxy/galaxy-dist/static/favicon.ico
> [L]
>
> RewriteRule ^/galaxy/robots.txt 
> /home/galaxy/galaxy-dist/static/robots.txt
> [L]
>
> RewriteRule ^(.*) http://localhost:8080$1 [P]
>
>
>
> Galaxy is visible at www.my_server_url.de but not at 
> www.my_server_url.de/galaxy
>
>
>
> Following the later URL I got this message:
>
> Proxy Error
>
> The proxy server received an invalid response from an upstream server.
> The proxy server could not handle the request GET /galaxy.
>
> Reason: DNS lookup failure for: localhost:8080http:
>
> 
> Apache/2.2.22 (Ubuntu) Server at www.my_server_url.de Port 80
>
> When I change the configuration like this: (make the second line a comment):
>
>
>
> RewriteEngine on
>
> #RewriteRule ^/galaxy$ /galaxy/ [R]
>
> RewriteRule ^/galaxy/static/style/(.*)
> /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
>
> RewriteRule ^/galaxy/static/scripts/(.*)
> /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L]
>
> RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 
> [L]
>
> RewriteRule ^/galaxy/favicon.ico 
> /home/galaxy/galaxy-dist/static/favicon.ico
> [L]
>
> RewriteRule ^/galaxy/robots.txt 
> /home/galaxy/galaxy-dist/static/robots.txt
> [L]
>
> RewriteRule ^(.*) http://localhost:8080$1 [P]
>
>
>
> Galaxy is visible both at www.my_server_url.de and at 
> www.my_server_url.de/galaxy
>
>
>
> When I completely remove this part, the “It works!” standard page of 
> apache is displayed.
>
>
>
> The configuration in my universe.ini is as follows:
>
> host = 127.0.0.1
>
>
>
> [filter:proxy-prefix]
>
> use = egg:PasteDeploy#prefix
>
> prefix = /galaxy
>
>
>
> [app:main]
>
> filter-with = proxy-prefix
>
> cookie_path = /galaxy
>
>
>
> Can you please help me with this issue?
>
> I want to see the “It works!” page at www.my_server_url.de and galaxy 
> only at www.my_server_urla.de/galaxy.
>
>
>
> Thanks in advance!
>
>
>
> Kind regards
>
> Matthias Enders
>
>
> ___
> 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:
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/

___
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:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Installing galaxy with Apache

[John Chilton]

Hmm... sorry for the delay I hope you got this to work. I feel like
someone should respond to this but it is difficult to remotely debug
web server configuration issues.

Should your apache config line:

RewriteRule ^(.*) http://localhost:8080$1 [P]

be:

RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]

instead?

That is the only guess I have. Thanks for your interest in deploying Galaxy.

-John


On Mon, Jun 2, 2014 at 7:37 AM, Matthias Enders
 wrote:
> Hi,
>
>
>
> this thread is likely related to this one:
>
>
>
> http://user.list.galaxyproject.org/Installing-galaxy-with-Apache-td4654499.html
>
>
>
> I installed Galaxy on a Ubuntu Server 12.04 system. I followed the
> instruction on the link mentioned above and this one:
>
> https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
>
>
>
> Now my issue is:
>
>
>
> When I got this configuration in my /etc/apache2/sites-available/default :
>
>
>
> RewriteEngine on
>
> RewriteRule ^/galaxy$ /galaxy/ [R]
>
> RewriteRule ^/galaxy/static/style/(.*)
> /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
>
> RewriteRule ^/galaxy/static/scripts/(.*)
> /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L]
>
> RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L]
>
> RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico
> [L]
>
> RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt
> [L]
>
> RewriteRule ^(.*) http://localhost:8080$1 [P]
>
>
>
> Galaxy is visible at www.my_server_url.de but not at
> www.my_server_url.de/galaxy
>
>
>
> Following the later URL I got this message:
>
> Proxy Error
>
> The proxy server received an invalid response from an upstream server.
> The proxy server could not handle the request GET /galaxy.
>
> Reason: DNS lookup failure for: localhost:8080http:
>
> 
> Apache/2.2.22 (Ubuntu) Server at www.my_server_url.de Port 80
>
> When I change the configuration like this: (make the second line a comment):
>
>
>
> RewriteEngine on
>
> #RewriteRule ^/galaxy$ /galaxy/ [R]
>
> RewriteRule ^/galaxy/static/style/(.*)
> /home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
>
> RewriteRule ^/galaxy/static/scripts/(.*)
> /home/galaxy/galaxy-dist/static/scripts/packed/$1 [L]
>
> RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L]
>
> RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico
> [L]
>
> RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt
> [L]
>
> RewriteRule ^(.*) http://localhost:8080$1 [P]
>
>
>
> Galaxy is visible both at www.my_server_url.de and at
> www.my_server_url.de/galaxy
>
>
>
> When I completely remove this part, the “It works!” standard page of apache
> is displayed.
>
>
>
> The configuration in my universe.ini is as follows:
>
> host = 127.0.0.1
>
>
>
> [filter:proxy-prefix]
>
> use = egg:PasteDeploy#prefix
>
> prefix = /galaxy
>
>
>
> [app:main]
>
> filter-with = proxy-prefix
>
> cookie_path = /galaxy
>
>
>
> Can you please help me with this issue?
>
> I want to see the “It works!” page at www.my_server_url.de and galaxy only
> at www.my_server_urla.de/galaxy.
>
>
>
> Thanks in advance!
>
>
>
> Kind regards
>
> Matthias Enders
>
>
> ___
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[galaxy-dev] Installing galaxy with Apache

[Matthias Enders]

Hi,

this thread is likely related to this one:

http://user.list.galaxyproject.org/Installing-galaxy-with-Apache-td4654499.html

I installed Galaxy on a Ubuntu Server 12.04 system. I followed the instruction 
on the link mentioned above and this one:
https://wiki.galaxyproject.org/Admin/Config/ApacheProxy

Now my issue is:

When I got this configuration in my /etc/apache2/sites-available/default :

RewriteEngine on
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*) 
/home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/scripts/(.*) 
/home/galaxy/galaxy-dist/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L]
RewriteRule ^(.*) http://localhost:8080$1 [P]

Galaxy is visible at www.my_server_url.de but not 
at www.my_server_url.de/galaxy

Following the later URL I got this message:
Proxy Error

The proxy server received an invalid response from an upstream server.
The proxy server could not handle the request GET 
/galaxy.

Reason: DNS lookup failure for: localhost:8080http:


Apache/2.2.22 (Ubuntu) Server at www.my_server_url.de Port 80


When I change the configuration like this: (make the second line a comment):

RewriteEngine on
#RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*) 
/home/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/scripts/(.*) 
/home/galaxy/galaxy-dist/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy/static/(.*) /home/galaxy/galaxy-dist/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico /home/galaxy/galaxy-dist/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /home/galaxy/galaxy-dist/static/robots.txt [L]
RewriteRule ^(.*) http://localhost:8080$1 [P]

Galaxy is visible both at www.my_server_url.de and 
at www.my_server_url.de/galaxy

When I completely remove this part, the "It works!" standard page of apache is 
displayed.

The configuration in my universe.ini is as follows:
host = 127.0.0.1

[filter:proxy-prefix]
use = egg:PasteDeploy#prefix
prefix = /galaxy

[app:main]
filter-with = proxy-prefix
cookie_path = /galaxy

Can you please help me with this issue?
I want to see the "It works!" page at 
www.my_server_url.de and galaxy only at 
www.my_server_urla.de/galaxy.

Thanks in advance!

Kind regards
Matthias Enders
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Re: [galaxy-dev] Installing Galaxy behind an Apache proxy using mod_auth_cas for user auth

[Sandra Gesing]

Dear all,

I have found a solution but I can unfortunately not explain why your solution 
on the Admin pages is not working. The following entries in httpd.conf solved 
the problem in our environment. Maybe this is useful for other CAS users.

Best,
Sandra

RewriteEngine on

  # Define the authentication method
  AuthType CAS
  AuthName Galaxy
  Require valid-user

# Proxy Configurations
ProxyVia On
ProxyPassInterpolateEnv On

   Order allow,deny
   Allow from all

ProxyPass / http://galaxy.crc.nd.edu:8080/
ProxyPassReverse / http://galaxy.crc.nd.edu:8080/
RequestHeader set REMOTE_USER %{REMOTE_USER}s
SSLProxyEngine On
AllowCONNECT 8080

RewriteRule ^(.*) http://galaxy.crc.nd.edu:8080$1 [P]


From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] 
On Behalf Of Sandra Gesing [sandra.ges...@nd.edu]
Sent: Tuesday, November 05, 2013 5:46 PM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Installing Galaxy behind an Apache proxy using 
mod_auth_cas for user auth

Dear all,

I would like to set up a local Galaxy instance behind an Apache server with our 
local CAS for authentication.

It would be great if you could give me a hint for the httpd.conf. I have the 
problem that after authenticating against CAS in the browser, I get following 
error message and REMOTE_USER doesn't seem to be in the HTTP header for Galaxy 
(I can see the REMOTE_USER in the access_log of Apache but not any more in 
paster.log of Galaxy).
"Access to Galaxy is denied
Galaxy is configured to authenticate users via an external method (such as HTTP 
authentication in Apache), but a username was not provided by the upstream 
(proxy) server. This is generally due to a misconfiguration in the upstream 
server."

I know that the same question was already asked in the following post but I 
haven't seen an option to extend the post and I haven't found an answer.
http://dev.list.galaxyproject.org/Installing-Galaxy-behind-an-Apache-proxy-using-mod-auth-cas-for-user-auth-tt4660837.html#none

Any help is much appreciated.

Many thanks,
Sandra

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[galaxy-dev] Installing Galaxy behind an Apache proxy using mod_auth_cas for user auth

[Sandra Gesing]

Dear all,

I would like to set up a local Galaxy instance behind an Apache server with our 
local CAS for authentication.

It would be great if you could give me a hint for the httpd.conf. I have the 
problem that after authenticating against CAS in the browser, I get following 
error message and REMOTE_USER doesn't seem to be in the HTTP header for Galaxy 
(I can see the REMOTE_USER in the access_log of Apache but not any more in 
paster.log of Galaxy).
"Access to Galaxy is denied
Galaxy is configured to authenticate users via an external method (such as HTTP 
authentication in Apache), but a username was not provided by the upstream 
(proxy) server. This is generally due to a misconfiguration in the upstream 
server."

I know that the same question was already asked in the following post but I 
haven't seen an option to extend the post and I haven't found an answer. 
http://dev.list.galaxyproject.org/Installing-Galaxy-behind-an-Apache-proxy-using-mod-auth-cas-for-user-auth-tt4660837.html#none

Any help is much appreciated.

Many thanks,
Sandra

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[galaxy-dev] Installing Galaxy behind an Apache proxy using mod_auth_cas for user auth

[Steve Harper]

I'm trying to install Galaxy behind an Apache proxy using mod_auth_cas 
for user authentication.  I've got a ways in but am now stuck with 
galaxy not getting the REMOTE_USER.  Has anyone deployed with this module?


I have use_remote_user = true on in my universe_wsgi.ini along with a 
valid maildomain.


Here's my apache config:

NameVirtualHost galaxy.utah.edu:80
NameVirtualHost galaxy.utah.edu:443

CASLoginURL https://go.utah.edu/cas/login
CASValidateURL https://go.utah.edu/cas/serviceValidate
CASValidateServer Off
CASAllowWildcardCert On
CASCertificatePath /etc/pki/tls/certs/ca-bundle.trust.crt
CASCookiePath /var/run/mod_auth_cas/
CASTimeout 3600
CASIdleTimeout 1800
CASDebug On


   RedirectPermanent / https://galaxy.utah.edu/



   SSLEngine on
   SSLProtocol -ALL +SSLv3 +TLSv1
   SSLCipherSuite HIGH:-aNULL:-eNULL

   #   Export the SSL environment variables to scripts
   
   SSLOptions +StdEnvVars
   

   #   Protocol adjustments for broken clients
   SetEnvIf User-Agent ".*MSIE.*" \
nokeepalive ssl-unclean-shutdown \
downgrade-1.0 force-response-1.0

   SSLCertificateFile  /etc/pki/tls/certs/wildcard.utah.edu.crt
   SSLCertificateKeyFile   /etc/pki/tls/certs/wildcard.utah.edu.key
   SSLCertificateChainFile /etc/pki/tls/certs/gd_bundle.crt


  http://localhost:8080>
  Order deny,allow
  Allow from all
  
  RewriteEngine on


  
AuthType CAS
AuthName Galaxy
Require valid-user

#CASAuthNHeader REMOTE_SHMUSER

# Take the $REMOTE_USER environment variable and set it as a header 
in the proxy request.

RewriteCond %{IS_SUBREQ} ^false$
RewriteCond %{LA-U:REMOTE_USER} (.+)
#RewriteCond %{LA-U:REMOTE_SHMUSER} (.+)
RewriteRule . - [E=RU:%1]
RequestHeader set REMOTE_USER %{RU}e

XSendFile on
XSendFilePath /
# Compress all uncompressed content.
SetOutputFilter DEFLATE
SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary
SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary
SetEnvIfNoCase Request_URI /history/export_archive no-gzip dont-vary

RequestHeader set X-URL-SCHEME https
  
  
# Allow browsers to cache everything from /static for 6 hours
ExpiresActive On
ExpiresDefault "access plus 6 hours"
  

  ServerName galaxy.utah.edu
  RewriteRule ^/static/style/(.*) 
/uufs/utah.edu/sys/pkg/galaxy/std/static/june_2007_style/blue/$1 [L]
  RewriteRule ^/static/scripts/(.*) 
/uufs/utah.edu/sys/pkg/galaxy/std/static/scripts/packed/$1 [L]

  RewriteRule ^/static/(.*) /uufs/utah.edu/sys/pkg/galaxy/std/static/$1 [L]
  RewriteRule ^/favicon.ico 
/uufs/utah.edu/sys/pkg/galaxy/std/static/favicon.ico [L]
  RewriteRule ^/robots.txt 
/uufs/utah.edu/sys/pkg/galaxy/std/static/robots.txt [L]

  RewriteRule ^(.*) http://localhost:8080$1 [P]



Any help is appreciated.

Steve Harper
Systems Administrator
Center for High Performance Computing
University of Utah
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Re: [galaxy-dev] Installing Galaxy EC2

[Daniel Gorelik]

Hello,

Thanks all, but it it turns out my problem was that the line saying to use the 
0.0.0.0 host was commented out.. That was stupid..

Thank you,
Daniel

On Jun 11, 2013, at 6:46 AM, Quang Trinh  wrote:

> Hi Dan and Joachim
>   You can also try what my students put together, which is based on a config 
> file and more simple.
> 
> https://github.com/modENCODE-DCC/Galaxy/blob/master/docs/README.how.to.launch.Galaxy
> 
> Thanks,
> 
> Q
> 
> 
> 
> 
> 
> On Tue, Jun 11, 2013 at 3:30 AM, Joachim Jacob | VIB |  
> wrote:
> Hi Daniel,
> 
> Make also sure you use correct firewall settings ('security groups') in EC2. 
> They are described the Galaxy wiki 
> (http://wiki.galaxyproject.org/CloudMan/AWS/GettingStarted?highlight=%28security%29|%28group%29),
>  but there are some small differences with the setting applied by CloudLaunch 
> (http://dev.list.galaxyproject.org/Cloudman-missing-security-rules-in-wiki-page-td4659826.html#a4659902)
> 
> Set by CloudLaunch (during my latest launch):
> Ports   ProtocolSource  CloudMan
> 1-65535 tcp sg-61ba790a
> *1-65535 udp sg-61ba790a *
> *-1  icmpsg-61ba790a *
> 20-21   tcp 0.0.0.0/0 
> 22  tcp 0.0.0.0/0 
> 80  tcp 0.0.0.0/0 
> 3-30100 tcp 0.0.0.0/0 
> 42284   tcp 0.0.0.0/0 
> 
> 
> Cheers,
> Joachim
> 
> Joachim Jacob
> Contact details: http://www.bits.vib.be/index.php/about/80-team
> 
> 
> On 06/10/2013 10:54 PM, Daniel Blankenberg wrote:
> Hi Daniel,
> 
> This should work fine. You'll need to make sure that you have the host 
> setting in your universe_wsgi.ini like:
> 
> host = 0.0.0.0
> 
> and that the port 8080 is open/accessible in the security group settings for 
> the instance in AWS.
> 
> 
> Thanks for using Galaxy,
> 
> Dan
> 
> On Jun 10, 2013, at 4:42 PM, Daniel Gorelik wrote:
> 
> Hello all,
> 
> I have a question: does anyone know if it is possible to install Galaxy on an 
> EC2 instance as you would on a local machine, not using CloudMan, and then 
> view it in the web browser by going to public_ip:8080? I have been trying and 
> it has not been working for me.
> 
> 
> Thanks so much!
> ___
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> 
> 
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Re: [galaxy-dev] Installing Galaxy EC2

[Joachim Jacob | VIB |]

Hi Daniel,

Make also sure you use correct firewall settings ('security groups') in 
EC2. They are described the Galaxy wiki 
(http://wiki.galaxyproject.org/CloudMan/AWS/GettingStarted?highlight=%28security%29|%28group%29), 
but there are some small differences with the setting applied by 
CloudLaunch 
(http://dev.list.galaxyproject.org/Cloudman-missing-security-rules-in-wiki-page-td4659826.html#a4659902)


Set by CloudLaunch (during my latest launch):
Ports   ProtocolSource  CloudMan
1-65535 tcp sg-61ba790a
*1-65535 udp sg-61ba790a *
*-1  icmpsg-61ba790a *
20-21   tcp 0.0.0.0/0 
22  tcp 0.0.0.0/0 
80  tcp 0.0.0.0/0 
3-30100 tcp 0.0.0.0/0 
42284   tcp 0.0.0.0/0 


Cheers,
Joachim

Joachim Jacob
Contact details: http://www.bits.vib.be/index.php/about/80-team


On 06/10/2013 10:54 PM, Daniel Blankenberg wrote:

Hi Daniel,

This should work fine. You'll need to make sure that you have the host 
setting in your universe_wsgi.ini like:


host = 0.0.0.0

and that the port 8080 is open/accessible in the security group 
settings for the instance in AWS.



Thanks for using Galaxy,

Dan

On Jun 10, 2013, at 4:42 PM, Daniel Gorelik wrote:


Hello all,

I have a question: does anyone know if it is possible to install 
Galaxy on an EC2 instance as you would on a local machine, not using 
CloudMan, and then view it in the web browser by going to 
public_ip:8080? I have been trying and it has not been working for me.



Thanks so much!
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Re: [galaxy-dev] Installing Galaxy EC2

[Daniel Blankenberg]

Hi Daniel,

This should work fine. You'll need to make sure that you have the host setting 
in your universe_wsgi.ini like:

host = 0.0.0.0

and that the port 8080 is open/accessible in the security group settings for 
the instance in AWS.


Thanks for using Galaxy,

Dan

On Jun 10, 2013, at 4:42 PM, Daniel Gorelik wrote:

> Hello all,
> 
> I have a question: does anyone know if it is possible to install Galaxy on an 
> EC2 instance as you would on a local machine, not using CloudMan, and then 
> view it in the web browser by going to public_ip:8080? I have been trying and 
> it has not been working for me.
> 
> 
> Thanks so much!
> ___
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[galaxy-dev] Installing Galaxy EC2

[Daniel Gorelik]

Hello all,

I have a question: does anyone know if it is possible to install Galaxy on an 
EC2 instance as you would on a local machine, not using CloudMan, and then view 
it in the web browser by going to public_ip:8080? I have been trying and it has 
not been working for me.


Thanks so much!
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Re: [galaxy-dev] installing galaxy

[מירב .]

It worked!! Thank you very mach

Merav


2013/5/29 Ross 

> Hi, Merav.
> A fully functional Galaxy server relies on a lot of third party software
> and the error message you see is probably because you do not have samtools
> available - the upload process needs it to make an index for your bam file.
> So the solution may be to install the samtools package - eg for ubuntu
> something like:
> sudo apt-get install samtools
>
> After that, if you execute
> samtools
> at a console, you should see something like:
>
> rlazarus@iaas1-int:~$ samtools
>
> Program: samtools (Tools for alignments in the SAM format)
> Version: 0.1.18 (r982:295)
>
> Usage:   samtools  [options]
>
> Command: viewSAM<->BAM conversion
>  sortsort alignment file
>  mpileup multi-way pileup
>
>
>
> Please take a look at
> http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
>
>
>
>
>
> On Wed, May 29, 2013 at 8:00 PM, מירב .  wrote:
>
>> hello,
>>
>> I am installing  galaxy locally.
>> I tried to upload a  ".bam" file and I got this message:
>>
>> Traceback (most recent call last):
>>   File "/home/user/galaxy_project/tools/data_source/upload.py", line 386, in 
>> 
>> __main__()
>>   File "/home/user/galaxy_project/tools/data_source/upload.py", line 375, in 
>> __main__
>> add_file( dataset, registry, json_file, output_path )
>>   File "/home/user/galaxy_project/tools/data_source/upload.py", line 314, in 
>> add_file
>> if link_data_only == 'copy_files' and 
>> datatype.dataset_content_needs_grooming( output_path ):
>>   File "/home/user/galaxy_project/lib/galaxy/datatypes/binary.py", line 113, 
>> in dataset_content_needs_grooming
>> version = self._get_samtools_version()
>>   File "/home/user/galaxy_project/lib/galaxy/datatypes/binary.py", line 97, 
>> in _get_samtools_version
>> output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, 
>> stdout=subprocess.PIPE ).communicate()[1]
>>   File "/usr/lib/python2.7/subprocess.py", line 679, in __init__
>> errread, errwrite)
>>   File "/usr/lib/python2.7/subprocess.py", line 1259, in _execute_child
>> raise child_exception
>> OSError: [Errno 2] No such file or directory
>>
>>
>> This file uploaded  successfully, to the galaxy on the net.
>>
>> what can it be?
>>
>>  thanks for your help
>>
>> merav
>>
>>
>>
>>
>>
>>
>> ___
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>>
>
>
>
> --
> Ross Lazarus MBBS MPH;
> Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
> http://scholar.google.com/citations?hl=en&user=UCUuEM4J
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Re: [galaxy-dev] installing galaxy

[Ross]

Hi, Merav.
A fully functional Galaxy server relies on a lot of third party software
and the error message you see is probably because you do not have samtools
available - the upload process needs it to make an index for your bam file.
So the solution may be to install the samtools package - eg for ubuntu
something like:
sudo apt-get install samtools

After that, if you execute
samtools
at a console, you should see something like:

rlazarus@iaas1-int:~$ samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.18 (r982:295)

Usage:   samtools  [options]

Command: viewSAM<->BAM conversion
 sortsort alignment file
 mpileup multi-way pileup



Please take a look at
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies





On Wed, May 29, 2013 at 8:00 PM, מירב .  wrote:

> hello,
>
> I am installing  galaxy locally.
> I tried to upload a  ".bam" file and I got this message:
>
> Traceback (most recent call last):
>   File "/home/user/galaxy_project/tools/data_source/upload.py", line 386, in 
> 
> __main__()
>   File "/home/user/galaxy_project/tools/data_source/upload.py", line 375, in 
> __main__
> add_file( dataset, registry, json_file, output_path )
>   File "/home/user/galaxy_project/tools/data_source/upload.py", line 314, in 
> add_file
> if link_data_only == 'copy_files' and 
> datatype.dataset_content_needs_grooming( output_path ):
>   File "/home/user/galaxy_project/lib/galaxy/datatypes/binary.py", line 113, 
> in dataset_content_needs_grooming
> version = self._get_samtools_version()
>   File "/home/user/galaxy_project/lib/galaxy/datatypes/binary.py", line 97, 
> in _get_samtools_version
> output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, 
> stdout=subprocess.PIPE ).communicate()[1]
>   File "/usr/lib/python2.7/subprocess.py", line 679, in __init__
> errread, errwrite)
>   File "/usr/lib/python2.7/subprocess.py", line 1259, in _execute_child
> raise child_exception
> OSError: [Errno 2] No such file or directory
>
>
> This file uploaded  successfully, to the galaxy on the net.
>
> what can it be?
>
>  thanks for your help
>
> merav
>
>
>
>
>
>
> ___
> 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:
>   http://lists.bx.psu.edu/
>
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>   http://galaxyproject.org/search/mailinglists/
>



-- 
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=en&user=UCUuEM4J
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[galaxy-dev] installing galaxy

[מירב .]

hello,

I am installing  galaxy locally.
I tried to upload a  ".bam" file and I got this message:

Traceback (most recent call last):
  File "/home/user/galaxy_project/tools/data_source/upload.py", line
386, in 
__main__()
  File "/home/user/galaxy_project/tools/data_source/upload.py", line
375, in __main__
add_file( dataset, registry, json_file, output_path )
  File "/home/user/galaxy_project/tools/data_source/upload.py", line
314, in add_file
if link_data_only == 'copy_files' and
datatype.dataset_content_needs_grooming( output_path ):
  File "/home/user/galaxy_project/lib/galaxy/datatypes/binary.py",
line 113, in dataset_content_needs_grooming
version = self._get_samtools_version()
  File "/home/user/galaxy_project/lib/galaxy/datatypes/binary.py",
line 97, in _get_samtools_version
output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE,
stdout=subprocess.PIPE ).communicate()[1]
  File "/usr/lib/python2.7/subprocess.py", line 679, in __init__
errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1259, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory


This file uploaded  successfully, to the galaxy on the net.

what can it be?

 thanks for your help

merav
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Re: [galaxy-dev] Installing Galaxy on ARM Architecture

[Carlos Borroto]

Hi Shun,

Would you please share which third-party tools you are able to compile
on ARM? I'll be very interested in knowing about that. I'm thinking on
things like samtools, bowtie, tophat, cufflinks, bwa, ncbi_blast, etc.

Thanks,
Carlos

On Fri, Feb 22, 2013 at 10:51 AM, Shun Liang  wrote:
> Hi Nate,
>
> After terminating the process which was listening 8080 I am now able to 
> launch Galaxy.
>
>
> Many thanks for you help,
> Shun
> 
> From: Nate Coraor [n...@bx.psu.edu]
> Sent: 22 February 2013 15:31
> To: Shun Liang
> Cc: James Taylor; galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Installing Galaxy on ARM Architecture
>
> On Feb 22, 2013, at 10:21 AM, Shun Liang wrote:
>
>> Hi Nate,
>>
>> After scramble,py failed, I ran
>>
>> $ python ./scripts/scramble.py -e bx_python
>>
>> and bx_python seems to be built without any problem:
>>
>> ...
>> writing build/bdist.linux-armv7l/egg/EGG-INFO/native_libs.txt
>> creating dist
>> creating 'dist/bx_python-0.7.1_7b95ff194725-py2.7-linux-armv7l-ucs4.egg' and 
>> adding 'build/bdist.linux-armv7l/egg' to it
>> removing 'build/bdist.linux-armv7l/egg' (and everything under it)
>> scramble(): Copied egg to:
>>  
>> /nfs/users/galaxy_dist/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-armv7l-ucs4.egg
>>
>>
>> ...and I then reran
>>
>> $ python ./scripts/scramble.py
>>
>> and it shows all eggs already exist. Then I ran
>
>
> This is a good sign.
>
>> $ sh run.sh
>>
>> to launch Galaxy, without making any change to universe_wsgi.ini. The launch 
>> of Galaxy failed with the following error message:
>>
>> ...
>> galaxy.webapps.galaxy.buildapp DEBUG 2013-02-22 15:14:03,077 Enabling 
>> 'Request ID' middleware
>> Starting server in PID 19121.
>> Traceback (most recent call last):
>>  File "./scripts/paster.py", line 33, in 
>>serve.run()
>>  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 
>> 1056, in run
>>invoke(command, command_name, options, args[1:])
>>  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 
>> 1062, in invoke
>>exit_code = runner.run(args)
>>  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 
>> 227, in run
>>result = self.command()
>>  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 
>> 677, in command
>>serve()
>>  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 
>> 661, in serve
>>server(app)
>>  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/loadwsgi.py", line 
>> 292, in server_wrapper
>>**context.local_conf)
>>  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/loadwsgi.py", line 
>> 97, in fix_call
>>val = callable(*args, **kw)
>>  File 
>> "/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
>> line 1342, in server_runner
>>serve(wsgi_app, **kwargs)
>>  File 
>> "/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
>> line 1291, in serve
>>request_queue_size=request_queue_size)
>>  File 
>> "/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
>> line 1134, in __init__
>>request_queue_size=request_queue_size)
>>  File 
>> "/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
>> line 1113, in __init__
>>request_queue_size=request_queue_size)
>>  File 
>> "/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
>> line 328, 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
>
> This means that something is already listening on the port Galaxy is trying 
> to use.  Assuming you did not change the port in universe_w

Re: [galaxy-dev] Installing Galaxy on ARM Architecture

[Shun Liang]

Hi Nate,

After terminating the process which was listening 8080 I am now able to launch 
Galaxy.


Many thanks for you help,
Shun

From: Nate Coraor [n...@bx.psu.edu]
Sent: 22 February 2013 15:31
To: Shun Liang
Cc: James Taylor; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Installing Galaxy on ARM Architecture

On Feb 22, 2013, at 10:21 AM, Shun Liang wrote:

> Hi Nate,
>
> After scramble,py failed, I ran
>
> $ python ./scripts/scramble.py -e bx_python
>
> and bx_python seems to be built without any problem:
>
> ...
> writing build/bdist.linux-armv7l/egg/EGG-INFO/native_libs.txt
> creating dist
> creating 'dist/bx_python-0.7.1_7b95ff194725-py2.7-linux-armv7l-ucs4.egg' and 
> adding 'build/bdist.linux-armv7l/egg' to it
> removing 'build/bdist.linux-armv7l/egg' (and everything under it)
> scramble(): Copied egg to:
>  
> /nfs/users/galaxy_dist/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-armv7l-ucs4.egg
>
>
> ...and I then reran
>
> $ python ./scripts/scramble.py
>
> and it shows all eggs already exist. Then I ran


This is a good sign.

> $ sh run.sh
>
> to launch Galaxy, without making any change to universe_wsgi.ini. The launch 
> of Galaxy failed with the following error message:
>
> ...
> galaxy.webapps.galaxy.buildapp DEBUG 2013-02-22 15:14:03,077 Enabling 
> 'Request ID' middleware
> Starting server in PID 19121.
> Traceback (most recent call last):
>  File "./scripts/paster.py", line 33, in 
>serve.run()
>  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 
> 1056, in run
>invoke(command, command_name, options, args[1:])
>  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 
> 1062, in invoke
>exit_code = runner.run(args)
>  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 
> 227, in run
>result = self.command()
>  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 
> 677, in command
>serve()
>  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 
> 661, in serve
>server(app)
>  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/loadwsgi.py", line 
> 292, in server_wrapper
>**context.local_conf)
>  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/loadwsgi.py", line 
> 97, in fix_call
>val = callable(*args, **kw)
>  File 
> "/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
> line 1342, in server_runner
>serve(wsgi_app, **kwargs)
>  File 
> "/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
> line 1291, in serve
>request_queue_size=request_queue_size)
>  File 
> "/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
> line 1134, in __init__
>request_queue_size=request_queue_size)
>  File 
> "/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
> line 1113, in __init__
>request_queue_size=request_queue_size)
>  File 
> "/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", 
> line 328, 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

This means that something is already listening on the port Galaxy is trying to 
use.  Assuming you did not change the port in universe_wsgi.ini, you can 
determine what process it is with `lsof -i :8080`.  Or you could change the 
port in universe_wsgi.ini to something else.

--nate

> galaxy.jobs.manager INFO 2013-02-22 15:14:03,134 sending stop signal to 
> worker thread
> galaxy.jobs.manager INFO 2013-02-22 15:14:03,135 job manager queue stopped
> galaxy.jobs.manager INFO 2013-02-22 15:14:03,135 sending stop signal to 
> worker thread
> galaxy.jobs.manager INFO 2013-02-22 15:14:03,135 job manager stop queue 
> stopped
> galaxy.jobs.handler INFO 2013-02-22 15:14:03,136 sending stop signal to 
> worker thread
> galaxy.jobs.handler INFO 2013-02-22 15:14:03,136 job handler queue stopped
> galaxy.jobs.runners.lwr INFO 2013-02-22 15:14:03,136 

Re: [galaxy-dev] Installing Galaxy on ARM Architecture

[Shun Liang]

Hi Nate,

After scramble,py failed, I ran

$ python ./scripts/scramble.py -e bx_python

and bx_python seems to be built without any problem:

...
writing build/bdist.linux-armv7l/egg/EGG-INFO/native_libs.txt
creating dist
creating 'dist/bx_python-0.7.1_7b95ff194725-py2.7-linux-armv7l-ucs4.egg' and 
adding 'build/bdist.linux-armv7l/egg' to it
removing 'build/bdist.linux-armv7l/egg' (and everything under it)
scramble(): Copied egg to:
  
/nfs/users/galaxy_dist/eggs/bx_python-0.7.1_7b95ff194725-py2.7-linux-armv7l-ucs4.egg


...and I then reran 

$ python ./scripts/scramble.py

 and it shows all eggs already exist. Then I ran 

 $ sh run.sh

to launch Galaxy, without making any change to universe_wsgi.ini. The launch of 
Galaxy failed with the following error message:

...
galaxy.webapps.galaxy.buildapp DEBUG 2013-02-22 15:14:03,077 Enabling 'Request 
ID' middleware
Starting server in PID 19121.
Traceback (most recent call last):
  File "./scripts/paster.py", line 33, in 
serve.run()
  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 
1056, in run
invoke(command, command_name, options, args[1:])
  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 
1062, in invoke
exit_code = runner.run(args)
  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 227, 
in run
result = self.command()
  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 677, 
in command
serve()
  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/serve.py", line 661, 
in serve
server(app)
  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/loadwsgi.py", line 
292, in server_wrapper
**context.local_conf)
  File "/nfs/users/galaxy_dist/lib/galaxy/util/pastescript/loadwsgi.py", line 
97, in fix_call
val = callable(*args, **kw)
  File 
"/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 
1342, in server_runner
serve(wsgi_app, **kwargs)
  File 
"/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 
1291, in serve
request_queue_size=request_queue_size)
  File 
"/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 
1134, in __init__
request_queue_size=request_queue_size)
  File 
"/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 
1113, in __init__
request_queue_size=request_queue_size)
  File 
"/nfs/users/galaxy_dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 
328, 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
galaxy.jobs.manager INFO 2013-02-22 15:14:03,134 sending stop signal to worker 
thread
galaxy.jobs.manager INFO 2013-02-22 15:14:03,135 job manager queue stopped
galaxy.jobs.manager INFO 2013-02-22 15:14:03,135 sending stop signal to worker 
thread
galaxy.jobs.manager INFO 2013-02-22 15:14:03,135 job manager stop queue stopped
galaxy.jobs.handler INFO 2013-02-22 15:14:03,136 sending stop signal to worker 
thread
galaxy.jobs.handler INFO 2013-02-22 15:14:03,136 job handler queue stopped
galaxy.jobs.runners.lwr INFO 2013-02-22 15:14:03,136 sending stop signal to 
worker threads
galaxy.jobs.runners.lwr INFO 2013-02-22 15:14:03,137 local job runner stopped
galaxy.jobs.runners.local INFO 2013-02-22 15:14:03,137 sending stop signal to 
worker threads
galaxy.jobs.runners.local INFO 2013-02-22 15:14:03,138 local job runner stopped
galaxy.jobs.handler INFO 2013-02-22 15:14:03,139 sending stop signal to worker 
thread
galaxy.jobs.handler INFO 2013-02-22 15:14:03,139 job handler stop queue stopped
Exception in thread LWRRunner.monitor_thread (most likely raised during 
interpreter shutdown):


I hope you find this information useful. Do you have any idea about what went 
wrong?


Many thanks,
Shun

From: Nate Coraor [n...@bx.psu.edu]
Sent: 21 February 2013 16:56
To: Shun Liang
Cc: James Taylor; galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Installing Galaxy on ARM Architecture

On Feb 21, 2013, at 11:47 AM, Shun Liang wrote:

> Sorry just forgot to CC the mailing list.
> 
>
> Hi James,
>
> I followed the manual installation instruction on 
> "https://bitbucket.org/james_taylor/bx-

Re: [galaxy-dev] Installing Galaxy on ARM Architecture

[Nate Coraor]

2-22 15:14:03,139 sending stop signal to 
> worker thread
> galaxy.jobs.handler INFO 2013-02-22 15:14:03,139 job handler stop queue 
> stopped
> Exception in thread LWRRunner.monitor_thread (most likely raised during 
> interpreter shutdown):
> 
> 
> I hope you find this information useful. Do you have any idea about what went 
> wrong?
> 
> 
> Many thanks,
> Shun
> 
> From: Nate Coraor [n...@bx.psu.edu]
> Sent: 21 February 2013 16:56
> To: Shun Liang
> Cc: James Taylor; galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Installing Galaxy on ARM Architecture
> 
> On Feb 21, 2013, at 11:47 AM, Shun Liang wrote:
> 
>> Sorry just forgot to CC the mailing list.
>> 
>> 
>> Hi James,
>> 
>> I followed the manual installation instruction on 
>> "https://bitbucket.org/james_taylor/bx-python/wiki/HowToInstall";, and 
>> surprisingly, bx-python seems to be built on the ARM server without any 
>> problem:
>> 
>> Installed 
>> /nfs/users/bx-python/lib/python/bx_python-0.7.1-py2.7-linux-armv7l.egg
>> Processing dependencies for bx-python==0.7.1
>> Finished processing dependencies for bx-python==0.7.1
> 
> Hi Shun.
> 
> I'm moving this over to galaxy-dev since it's about a local installation.
> 
> Galaxy's eggs lib isn't finding the egg you built because Galaxy adds the 
> Mercurial revision to the egg version, and then expects the egg to be 
> physically located in galaxy-dist/eggs/.  The library will be looking for:
> 
>bx_python-0.7.1_7b95ff194725-py2.7-linux-armv71.egg
> 
> If you are able to build it through scramble that would be ideal since it 
> handles that naming for you, and there will be other C-Extension eggs to 
> build under similar constraints.  There should have been an error earlier in 
> the scramble output with more details on why building bx-python failed.  If 
> you rerun scramble on just that egg, you should be able to recapture the 
> output:
> 
>  % python ./scripts/scramble.py -e bx_python
> 
> --nate
> 
>> 
>> 
>> 
>> Regards,
>> Shun
>> 
>> From: ja...@taylorlab.org [ja...@taylorlab.org] on behalf of James Taylor 
>> [ja...@jamestaylor.org]
>> Sent: 21 February 2013 16:07
>> To: Shun Liang
>> Cc: galaxy-u...@lists.bx.psu.edu
>> Subject: Re: [galaxy-user] Installing Galaxy on ARM Architecture
>> 
>> You are definitely in uncharted territory with an arm server. Can you
>> try building just bx-python itself and let us know what the errors
>> are?
>> 
>> --
>> James Taylor, Assistant Professor, Biology/CS, Emory University
>> 
>> 
>> On Thu, Feb 21, 2013 at 11:03 AM, Shun Liang  
>> wrote:
>>> Hi,
>>> 
>>> I am trying to install Galaxy on an ARMV7 architecture Linux server. I ran
>>> "run.sh" and failed because some of the python eggs could not be fetched. I
>>> then have a look at "http://eggs.galaxyproject.org/"; and I have realized
>>> there aren't any armv7 builds for those eggs.
>>> 
>>> I then decided to build (or scramble) the eggs on my own. I ran
>>> "scripts/scramble.py" and this also failed with the following message (after
>>> building a lot of things):
>>> 
>>> scramble(): Copied egg to:
>>> /nfs/users/galaxy_dist/eggs/twill-0.9-py2.7.egg
>>> Traceback (most recent call last):
>>> File "scripts/scramble.py", line 26, in 
>>>   eggs = c.scramble()
>>> File "/nfs/users/galaxy_dist/lib/galaxy/eggs/scramble.py", line 242, in
>>> scramble
>>>   raise last_exc # only 1 failure out of the crate, be more informative
>>> galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build
>>> failed for bx_python 0.7.1
>>> 
>>> 
>>> May I ask what may cause this problem? Have I done anything wrong? Or, is it
>>> even possible to install Galaxy on ARM architecture Linux?
>>> 
>>> 
>>> 
>>> Many thanks,
>>> Shun
>>> 
>>> 
>>> ___
>>> 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/
>> 
>> ___
>> 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/
> 
> 


___
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Re: [galaxy-dev] Installing Galaxy on ARM Architecture

[Nate Coraor]

On Feb 21, 2013, at 11:47 AM, Shun Liang wrote:

> Sorry just forgot to CC the mailing list.
> 
> 
> Hi James,
> 
> I followed the manual installation instruction on 
> "https://bitbucket.org/james_taylor/bx-python/wiki/HowToInstall";, and 
> surprisingly, bx-python seems to be built on the ARM server without any 
> problem:
> 
> Installed 
> /nfs/users/bx-python/lib/python/bx_python-0.7.1-py2.7-linux-armv7l.egg
> Processing dependencies for bx-python==0.7.1
> Finished processing dependencies for bx-python==0.7.1

Hi Shun.

I'm moving this over to galaxy-dev since it's about a local installation.

Galaxy's eggs lib isn't finding the egg you built because Galaxy adds the 
Mercurial revision to the egg version, and then expects the egg to be 
physically located in galaxy-dist/eggs/.  The library will be looking for:

bx_python-0.7.1_7b95ff194725-py2.7-linux-armv71.egg

If you are able to build it through scramble that would be ideal since it 
handles that naming for you, and there will be other C-Extension eggs to build 
under similar constraints.  There should have been an error earlier in the 
scramble output with more details on why building bx-python failed.  If you 
rerun scramble on just that egg, you should be able to recapture the output:

  % python ./scripts/scramble.py -e bx_python

--nate

> 
> 
> 
> Regards,
> Shun
> 
> From: ja...@taylorlab.org [ja...@taylorlab.org] on behalf of James Taylor 
> [ja...@jamestaylor.org]
> Sent: 21 February 2013 16:07
> To: Shun Liang
> Cc: galaxy-u...@lists.bx.psu.edu
> Subject: Re: [galaxy-user] Installing Galaxy on ARM Architecture
> 
> You are definitely in uncharted territory with an arm server. Can you
> try building just bx-python itself and let us know what the errors
> are?
> 
> --
> James Taylor, Assistant Professor, Biology/CS, Emory University
> 
> 
> On Thu, Feb 21, 2013 at 11:03 AM, Shun Liang  
> wrote:
>> Hi,
>> 
>> I am trying to install Galaxy on an ARMV7 architecture Linux server. I ran
>> "run.sh" and failed because some of the python eggs could not be fetched. I
>> then have a look at "http://eggs.galaxyproject.org/"; and I have realized
>> there aren't any armv7 builds for those eggs.
>> 
>> I then decided to build (or scramble) the eggs on my own. I ran
>> "scripts/scramble.py" and this also failed with the following message (after
>> building a lot of things):
>> 
>> scramble(): Copied egg to:
>>  /nfs/users/galaxy_dist/eggs/twill-0.9-py2.7.egg
>> Traceback (most recent call last):
>>  File "scripts/scramble.py", line 26, in 
>>eggs = c.scramble()
>>  File "/nfs/users/galaxy_dist/lib/galaxy/eggs/scramble.py", line 242, in
>> scramble
>>raise last_exc # only 1 failure out of the crate, be more informative
>> galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build
>> failed for bx_python 0.7.1
>> 
>> 
>> May I ask what may cause this problem? Have I done anything wrong? Or, is it
>> even possible to install Galaxy on ARM architecture Linux?
>> 
>> 
>> 
>> Many thanks,
>> Shun
>> 
>> 
>> ___
>> 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
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>> use the Galaxy Development list:
>> 
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>> please use the interface at:
>> 
>>  http://lists.bx.psu.edu/
> 
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Re: [galaxy-dev] Installing Galaxy and Hooking into a SGE Cluster

[greg]

On Fri, Aug 24, 2012 at 9:56 AM, Peter Cock  wrote:
> On Fri, Aug 24, 2012 at 1:25 PM, mailing list 
> aka Greg wrote:
>> Thanks Assaf.
>>
>> Would anyone know about my question 1?  If I install a local version
>> of Galaxy and connect it to our cluster, where is each user's
>> (uploaded?) data stored?  How will the cluster jobs be able to access
>> the data?
>
> By default, all the data is under a single folder, belonging to the
> galaxy Linux user account. We use /mnt/galaxy/galaxy-dist for
> this. In order that the cluster jobs can access the data, they must
> also be able to see this mount.

So can one user see another's files in your setup?  I'd prefer if each
user could only see and use his own files.

How do users get data into Galaxy in your system?

Thanks,

Greg


> Galaxy does have support for staging files between file systems,
> but the simpler approach of unified storage is recommended.
> See http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster
>
>> If anyone has installed galaxy and hooked it up to Sun Grid engine,
>> I'd love to hear from you.
>
> We're using Galaxy and SGE. You could run Galaxy on the SGE
> head node, but in our setup the Galaxy machine is just an SGE
> submit node (so it can submit jobs and check on them, i.e.
> you can use qsub and qstat from our Galaxy server).
>
> Peter
>
> P.S. It is very confusing that your emails give your name
> as "mailing list" rather than Greg.

I think I fixed this?
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Re: [galaxy-dev] Installing Galaxy and Hooking into a SGE Cluster

[Peter Cock]

On Fri, Aug 24, 2012 at 1:25 PM, mailing list 
aka Greg wrote:
> Thanks Assaf.
>
> Would anyone know about my question 1?  If I install a local version
> of Galaxy and connect it to our cluster, where is each user's
> (uploaded?) data stored?  How will the cluster jobs be able to access
> the data?

By default, all the data is under a single folder, belonging to the
galaxy Linux user account. We use /mnt/galaxy/galaxy-dist for
this. In order that the cluster jobs can access the data, they must
also be able to see this mount.

Galaxy does have support for staging files between file systems,
but the simpler approach of unified storage is recommended.
See http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster

> If anyone has installed galaxy and hooked it up to Sun Grid engine,
> I'd love to hear from you.

We're using Galaxy and SGE. You could run Galaxy on the SGE
head node, but in our setup the Galaxy machine is just an SGE
submit node (so it can submit jobs and check on them, i.e.
you can use qsub and qstat from our Galaxy server).

Peter

P.S. It is very confusing that your emails give your name
as "mailing list" rather than Greg.
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Re: [galaxy-dev] Installing Galaxy and Hooking into a SGE Cluster

[mailing list]

Thanks Assaf.

Would anyone know about my question 1?  If I install a local version
of Galaxy and connect it to our cluster, where is each user's
(uploaded?) data stored?  How will the cluster jobs be able to access
the data?

If anyone has installed galaxy and hooked it up to Sun Grid engine,
I'd love to hear from you.

Thanks,

Greg

On Thu, Aug 23, 2012 at 6:29 PM, Assaf Gordon  wrote:
> (Moving to Galaxy-dev, seems more appropriate).
>
> John Jones wrote, On 08/23/2012 05:29 PM:
>>
>> His original question was about getting Galaxy to recognise LDAP 
>> authentication and personal storage space rather than shared storage space 
>> as is usual with Galaxy.
>> Licensing only came into it because Greg wanted LDAP authentication to track 
>> individual user usage (for billing) and I questioned the legality of billing 
>> for the software used by Galaxy, as I'm sure some components have a 
>> non-commercial usage licence clause.
>>
>
> 1. Technically (billing on an SGE cluster):
>
> There's a script in "./contrib" called "collect_sge_job_timings.sh" .
> details are here:
> http://dev.list.galaxyproject.org/Detailed-SGE-timing-information-about-galaxy-jobs-tt4140860.html
>
> Assuming you're using PostgreSQL + SGE, it will give you what you want 
> (break-down of SGE jobs timings and Galaxy users).
>
> With little adaptation, you can use it to exact SGE JobID and Galaxy Tool-ID 
> / user ID.
>
> If you want to extract it directly from the galaxy database, then the 
> following SQL will get you started:
> ===
> select
>  email as "user",
>  tool_id as "tool",
>  job_runner_external_id as "SGE_ID"
> from
>  job, galaxy_user
> where
>  job.user_id = galaxy_user.id
>  and
>  job_runner_name like 'drmaa%'
>  ;
> ===
> "job_runner_external_ID" will be the SGE-ID, and once you have the list (per 
> each galaxy user), you can use "qacct" to get the information for the job, 
> then calculate the charges.
>
>
>
> 2. Legally:
> IANAL, but to the best of my (limited) understanding:
>
> 1. Galaxy itself (server code, etc.) - completely legal to run it 
> commercially, even charge money for it - it is licensed as a BSD/MIT style 
> license.
> 2. Individual tools:
> if the tools are GPL'd (e.g. bowtie, tophat, bwa, cufflinks) or BSD/MIT - 
> completely legal to run them commercially, and even charge money for them.
> if the tools use any special license that restrict commercial use (commonly 
> stated as "free for personal, academic, non-commercial use", e.g. Jim Kent's 
> UCSC Genome Browser tools) - then you can't use them in your commercial 
> company without buying a special license (not even internally).
>
> It's really not complicated at all, and most (if not all) tools that you 
> compile from source to install them will have a file called "license" or 
> "copying" that will tell you what is the license.
> If the tools didn't come with a source code, they are probably not 
> free/open-source for commercial use (e.g. - novoalign).
>
>
> 3. Morally:
> Anyone who thinks of free/open-source as "charity" is missing the point.
> There is no "charity", and it's perfectly legal, moral, and even recommended 
> to charge money when offering services that are based on free/open-source 
> tools - the requirement (when using GPL) is to give the source code to users 
> when they ask for it (and some other complications, don't want to start a 
> flame war here) - so if they don't want to pay $1,000 for your service - the 
> are more than welcomed to buy their own cluster and storage and servers and 
> run the program themselves - that is the whole point of free/open source. 
> There is not charity.
>
> When people write (and publish) software - they explicitly decide upon the 
> license they prefer, and they should know what are the affects of the license.
> For example, the Galaxy team released Galaxy under a permissive BSD/MIT style 
> license, so they were completely aware of the fact that not only Galaxy can 
> be incorporated into a commercial product, the license doesn't even require 
> the commercial company to release any code changes they make to Galaxy. It's 
> a conscious decision, not an after-thought, and not charity.
>
> (end of my rambling...)
>
> -gordon
>
>
>
>
>
>

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Re: [galaxy-dev] Installing Galaxy and Hooking into a SGE Cluster

[Assaf Gordon]

(Moving to Galaxy-dev, seems more appropriate).

John Jones wrote, On 08/23/2012 05:29 PM:
> 
> His original question was about getting Galaxy to recognise LDAP 
> authentication and personal storage space rather than shared storage space as 
> is usual with Galaxy.
> Licensing only came into it because Greg wanted LDAP authentication to track 
> individual user usage (for billing) and I questioned the legality of billing 
> for the software used by Galaxy, as I'm sure some components have a 
> non-commercial usage licence clause.
> 

1. Technically (billing on an SGE cluster):

There's a script in "./contrib" called "collect_sge_job_timings.sh" .
details are here:
http://dev.list.galaxyproject.org/Detailed-SGE-timing-information-about-galaxy-jobs-tt4140860.html

Assuming you're using PostgreSQL + SGE, it will give you what you want 
(break-down of SGE jobs timings and Galaxy users).

With little adaptation, you can use it to exact SGE JobID and Galaxy Tool-ID / 
user ID.

If you want to extract it directly from the galaxy database, then the following 
SQL will get you started:
===
select
 email as "user",
 tool_id as "tool", 
 job_runner_external_id as "SGE_ID"
from
 job, galaxy_user
where
 job.user_id = galaxy_user.id
 and
 job_runner_name like 'drmaa%'
 ;
===
"job_runner_external_ID" will be the SGE-ID, and once you have the list (per 
each galaxy user), you can use "qacct" to get the information for the job, then 
calculate the charges.



2. Legally:
IANAL, but to the best of my (limited) understanding:

1. Galaxy itself (server code, etc.) - completely legal to run it commercially, 
even charge money for it - it is licensed as a BSD/MIT style license.
2. Individual tools:
if the tools are GPL'd (e.g. bowtie, tophat, bwa, cufflinks) or BSD/MIT - 
completely legal to run them commercially, and even charge money for them.
if the tools use any special license that restrict commercial use (commonly 
stated as "free for personal, academic, non-commercial use", e.g. Jim Kent's 
UCSC Genome Browser tools) - then you can't use them in your commercial company 
without buying a special license (not even internally).

It's really not complicated at all, and most (if not all) tools that you 
compile from source to install them will have a file called "license" or 
"copying" that will tell you what is the license.
If the tools didn't come with a source code, they are probably not 
free/open-source for commercial use (e.g. - novoalign).


3. Morally:
Anyone who thinks of free/open-source as "charity" is missing the point.
There is no "charity", and it's perfectly legal, moral, and even recommended to 
charge money when offering services that are based on free/open-source tools - 
the requirement (when using GPL) is to give the source code to users when they 
ask for it (and some other complications, don't want to start a flame war here) 
- so if they don't want to pay $1,000 for your service - the are more than 
welcomed to buy their own cluster and storage and servers and run the program 
themselves - that is the whole point of free/open source. There is not charity.

When people write (and publish) software - they explicitly decide upon the 
license they prefer, and they should know what are the affects of the license.
For example, the Galaxy team released Galaxy under a permissive BSD/MIT style 
license, so they were completely aware of the fact that not only Galaxy can be 
incorporated into a commercial product, the license doesn't even require the 
commercial company to release any code changes they make to Galaxy. It's a 
conscious decision, not an after-thought, and not charity.

(end of my rambling...)

-gordon

 




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Re: [galaxy-dev] Installing Galaxy on Mac OS X 10.7: pyglet issue

[Nate Coraor]

On May 6, 2012, at 5:11 AM, Arnav Moudgil wrote:

> Hi folks,
> 
> I'm trying to install Galaxy locally on my Mac running OS X 10.7 and Python 
> 2.7.3. After cloning the repository and running sh run.sh the first time, the 
> following error occurs:
> 
> [Fetches series of eggs…]
> Fetch successful.
> Traceback (most recent call last):
>   File "./scripts/paster.py", line 34, in 
> command.run()
>   File 
> "/Users/username/Downloads/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
>  line 73, in run
> commands = get_commands()
>   File 
> "/Users/username/Downloads/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
>  line 115, in get_commands
> plugins = pluginlib.resolve_plugins(plugins)
>   File 
> "/Users/username/Downloads/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/pluginlib.py",
>  line 81, in resolve_plugins
> pkg_resources.require(plugin)
>   File "/Users/username/Downloads/galaxy-dist/lib/galaxy/eggs/__init__.py", 
> line 413, in require
> return pkg_resources.working_set.require( req_str )
>   File "/Users/username/Downloads/galaxy-dist/lib/pkg_resources.py", line 
> 666, in require
> needed = self.resolve(parse_requirements(requirements))
>   File "/Users/username/Downloads/galaxy-dist/lib/pkg_resources.py", line 
> 565, in resolve
> raise DistributionNotFound(req)  # XXX put more info here
> pkg_resources.DistributionNotFound: Not Found: pyglet-1.1.4-py2.6 (did you 
> run python setup.py develop?)
> 
> I have downloaded and installed pyglet for both Python 2.7 and 2.6 (both 
> versions are on my system, but 2.7 is default), and the error still persists. 
> Any ideas what's going on here?

Hi Arnav,

pyglet is not a Galaxy dependency, so I have no idea where that is coming from, 
but I suspect it has something to do with your python environment.  Could you 
set up a virtualenv as described here:

http://usegalaxy.org/production

And see if that makes a difference?

--nate

> 
> 
> Thanks!
> 
> ___
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> and other Galaxy lists, please use the interface at:
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[galaxy-dev] Installing Galaxy on Mac OS X 10.7: pyglet issue

[Arnav Moudgil]

Hi folks,  

I'm trying to install Galaxy locally on my Mac running OS X 10.7 and Python 
2.7.3. After cloning the repository and running sh run.sh the first time, the 
following error occurs:

[Fetches series of eggs…]
Fetch successful.
Traceback (most recent call last):
  File "./scripts/paster.py", line 34, in 
command.run()
  File 
"/Users/username/Downloads/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
 line 73, in run
commands = get_commands()
  File 
"/Users/username/Downloads/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
 line 115, in get_commands
plugins = pluginlib.resolve_plugins(plugins)
  File 
"/Users/username/Downloads/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/pluginlib.py",
 line 81, in resolve_plugins
pkg_resources.require(plugin)
  File "/Users/username/Downloads/galaxy-dist/lib/galaxy/eggs/__init__.py", 
line 413, in require
return pkg_resources.working_set.require( req_str )
  File "/Users/username/Downloads/galaxy-dist/lib/pkg_resources.py", line 666, 
in require
needed = self.resolve(parse_requirements(requirements))
  File "/Users/username/Downloads/galaxy-dist/lib/pkg_resources.py", line 565, 
in resolve
raise DistributionNotFound(req)  # XXX put more info here
pkg_resources.DistributionNotFound: Not Found: pyglet-1.1.4-py2.6 (did you run 
python setup.py develop?)

I have downloaded and installed pyglet for both Python 2.7 and 2.6 (both 
versions are on my system, but 2.7 is default), and the error still persists. 
Any ideas what's going on here?


Thanks!

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Re: [galaxy-dev] Installing Galaxy on local server

[Carlos Borroto]

Hi Toqa,

I think you would want to use "sh run.sh --daemon", so you don't have
to keep the cli session open. To stop the daemon then you would use
"sh run.sh --stop-daemon".

You could read much more about a production server installation at:
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server

Regards,
Carlos

On Tue, Nov 8, 2011 at 8:22 AM, Jennifer Jackson  wrote:
> Hello Tuqa,
>
> Galaxy will not stop by itself. That said, you will want to monitor the
> instance and any associated cluster, just as you would any other important
> processes.
>
> Please send all follow-up with a cc to the mailing list ("reply-all"). The
> development community is a great resource for administrative advice and they
> may have more to add to this reply, i.e. how stable they have found Galaxy
> to be under various conditions.
>
> Best,
>
> Jen
> Galaxy team
>
> On 11/8/11 4:01 AM, Toqa Manasrah wrote:
>>
>> Thank you so much,
>>
>> I did the installation and I ran it under my server.
>> I have one thing concerning about now. if u can help plz.
>>
>> how to run Galaxy in such way that the html interface will continuously
>> working and available for all users visiting the page?
>>
>> i mean how to guarantee that the "sh run.sh" will keep running without any
>> interrupt?
>>
>> Thank you,
>> Tuqa
>>
>> ________________
>> From: Jennifer Jackson [j...@bx.psu.edu]
>> Sent: Thursday, November 03, 2011 6:47 PM
>> To: Toqa Manasrah
>> Cc: galaxy-...@bx.psu.edu
>> Subject: Re: [galaxy-dev] Installing Galaxy on local server
>>
>> Hello Toqa,
>>
>>  From your description, this sounds like a local installation for the
>> Galaxy instance itself. Then you can add on a cluster (local or cloud)
>> as needed.
>>
>> Help is under "Deploy Galaxy" at http://wiki.g2.bx.psu.edu/
>> Also see the "Tool Shed" at http://wiki.g2.bx.psu.edu/Tool%20Shed
>>
>> Hopefully the documentation is helpful,
>>
>> Best,
>>
>> Jen
>> Galaxy team
>>
>> On 11/3/11 9:40 AM, Toqa Manasrah wrote:
>>>
>>> Hello,
>>>
>>> I am a graduate student at GSU. I am looking for installing GALAXY on
>>> our local server http://alla.cs.gsu.edu/~software. as a result I like my
>>> server homepage start with the GALAXY interface, like this one:
>>> http://rna1.engr.uconn.edu:7474/ . after that I wish to integrate some
>>> software tolls that we developed in ourdepartment. my primary question
>>> is which option Ihave to choose: Local or cloud?
>>>
>>> looking forward for your help and directions.
>>>
>>> Thank you.
>>>
>>> Tuqa
>>>
>>>
>>>
>>> ___
>>> 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:
>>>
>>>    http://lists.bx.psu.edu/
>>
>> --
>> Jennifer Jackson
>> http://usegalaxy.org
>> http://galaxyproject.org/wiki/Support
>>
>
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/wiki/Support
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>
>  http://lists.bx.psu.edu/
>

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Re: [galaxy-dev] Installing Galaxy on local server

[Jennifer Jackson]

Hello Tuqa,

Galaxy will not stop by itself. That said, you will want to monitor the 
instance and any associated cluster, just as you would any other 
important processes.


Please send all follow-up with a cc to the mailing list ("reply-all"). 
The development community is a great resource for administrative advice 
and they may have more to add to this reply, i.e. how stable they have 
found Galaxy to be under various conditions.


Best,

Jen
Galaxy team

On 11/8/11 4:01 AM, Toqa Manasrah wrote:

Thank you so much,

I did the installation and I ran it under my server.
I have one thing concerning about now. if u can help plz.

how to run Galaxy in such way that the html interface will continuously working 
and available for all users visiting the page?

i mean how to guarantee that the "sh run.sh" will keep running without any 
interrupt?

Thank you,
Tuqa


From: Jennifer Jackson [j...@bx.psu.edu]
Sent: Thursday, November 03, 2011 6:47 PM
To: Toqa Manasrah
Cc: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Installing Galaxy on local server

Hello Toqa,

  From your description, this sounds like a local installation for the
Galaxy instance itself. Then you can add on a cluster (local or cloud)
as needed.

Help is under "Deploy Galaxy" at http://wiki.g2.bx.psu.edu/
Also see the "Tool Shed" at http://wiki.g2.bx.psu.edu/Tool%20Shed

Hopefully the documentation is helpful,

Best,

Jen
Galaxy team

On 11/3/11 9:40 AM, Toqa Manasrah wrote:

Hello,

I am a graduate student at GSU. I am looking for installing GALAXY on
our local server http://alla.cs.gsu.edu/~software. as a result I like my
server homepage start with the GALAXY interface, like this one:
http://rna1.engr.uconn.edu:7474/ . after that I wish to integrate some
software tolls that we developed in ourdepartment. my primary question
is which option Ihave to choose: Local or cloud?

looking forward for your help and directions.

Thank you.

Tuqa



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http://galaxyproject.org/wiki/Support



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Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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Re: [galaxy-dev] Installing Galaxy on local server

[Jennifer Jackson]

Hello Toqa,

From your description, this sounds like a local installation for the 
Galaxy instance itself. Then you can add on a cluster (local or cloud) 
as needed.


Help is under "Deploy Galaxy" at http://wiki.g2.bx.psu.edu/
Also see the "Tool Shed" at http://wiki.g2.bx.psu.edu/Tool%20Shed

Hopefully the documentation is helpful,

Best,

Jen
Galaxy team

On 11/3/11 9:40 AM, Toqa Manasrah wrote:

Hello,

I am a graduate student at GSU. I am looking for installing GALAXY on
our local server http://alla.cs.gsu.edu/~software. as a result I like my
server homepage start with the GALAXY interface, like this one:
http://rna1.engr.uconn.edu:7474/ . after that I wish to integrate some
software tolls that we developed in ourdepartment. my primary question
is which option Ihave to choose: Local or cloud?

looking forward for your help and directions.

Thank you.

Tuqa



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Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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[galaxy-dev] Installing Galaxy on local server

[Toqa Manasrah]

Hello,



I am a graduate student at GSU. I am looking for installing GALAXY on our local 
server http://alla.cs.gsu.edu/~software. as a result I like my server homepage 
start with the GALAXY interface, like this one: 
http://rna1.engr.uconn.edu:7474/ . after that I wish to integrate some software 
tolls that we developed in our department. my primary question is which option 
I have to choose: Local or cloud?





looking forward for your help and directions.



Thank you.



Tuqa


___
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:

  http://lists.bx.psu.edu/

[galaxy-dev] Installing Galaxy on local server

[Toqa Manasrah]

Hello,



I am a graduate student at GSU. I am looking for installing GALAXY on our local 
server http://alla.cs.gsu.edu/~software. as a result I like my server homepage 
start with the GALAXY interface, like this one: 
http://rna1.engr.uconn.edu:7474/ . after that I wish to integrate some software 
tolls that we developed in our department. my primary question is which option 
I have to choose: Local or cloud?





looking forward for your help and directions.



Thank you.



Tuqa


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Please keep all replies on the list by using "reply all"
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