Re: [galaxy-dev] Manage API keys in admin panel
Ok, so I answer to myself. I created 2 template and 1 controller.
You need tu put the controller in
[galaxy_install_dir]/lib/galaxy/webapps/galaxy/controllers/userskeys.py
Contains the user interface in the Universe class
import glob
import logging
import os
import socket
import string
import random
import pprint
from galaxy import web
from galaxy import util, model
from galaxy.model.orm import and_
from galaxy.security.validate_user_input import validate_email,
validate_publicname, validate_password, transform_publicname
from galaxy.util.json import from_json_string, to_json_string
from galaxy.web import url_for
from galaxy.web.base.controller import BaseUIController,
UsesFormDefinitionsMixin
from galaxy.web.form_builder import CheckboxField, build_select_field
from galaxy.web.framework.helpers import time_ago, grids
from inspect import getmembers
log = logging.getLogger( __name__ )
require_login_template =
p
This %s has been configured such that only users who are logged in may
use it.%s
/p
p/
class UserOpenIDGrid( grids.Grid ):
use_panels = False
title = OpenIDs linked to your account
model_class = model.UserOpenID
template = '/user/openid_manage.mako'
default_filter = { openid : All }
default_sort_key = -create_time
columns = [
grids.TextColumn( OpenID URL, key=openid, link=( lambda x:
dict( action='openid_auth', login_button=Login, openid_url=x.openid if
not x.provider else '', openid_provider=x.provider, auto_associate=True ) )
),
grids.GridColumn( Created, key=create_time, format=time_ago ),
]
operations = [
grids.GridOperation( Delete, async_compatible=True ),
]
def build_initial_query( self, trans, **kwd ):
return trans.sa_session.query( self.model_class ).filter(
self.model_class.user_id == trans.user.id )
class User( BaseUIController, UsesFormDefinitionsMixin ):
user_openid_grid = UserOpenIDGrid()
installed_len_files = None
@web.expose
@web.require_login()
def api_keys( self, trans, cntrller, uid, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
uid = params.get('uid', uid)
pprint.pprint(uid)
if params.get( 'new_api_key_button', False ):
new_key = trans.app.model.APIKeys()
new_key.user_id = uid
new_key.key = trans.app.security.get_new_guid()
trans.sa_session.add( new_key )
trans.sa_session.flush()
message = Generated a new web API key
status = done
return trans.fill_template(
'webapps/galaxy/user/ok_admin_api_keys.mako',
cntrller=cntrller,
message=message,
status=status )
@web.expose
@web.require_login()
def all_users( self, trans, cntrller, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
users = []
for user in trans.sa_session.query( trans.app.model.User ) \
.filter(
trans.app.model.User.table.c.deleted==False ) \
.order_by(
trans.app.model.User.table.c.email ):
uid = int(user.id)
userkey =
for api_user in
trans.sa_session.query(trans.app.model.APIKeys) \
.filter(
trans.app.model.APIKeys.user_id == uid):
userkey = api_user.key
users.append({'uid':uid, 'email':user.email, 'key':userkey})
return trans.fill_template( 'webapps/galaxy/user/list_users.mako',
cntrller=cntrller,
users=users,
message=message,
status=status )
Then the 2 templates [galaxy_install_dir]/templates/webapps/galaxy/user/
The first one listing all the users with their keys
cat templates/webapps/galaxy/user/list_users.mako
%inherit file=/base.mako/
%if message:
${render_msg( message, status )}
%endif
%if users:
div class=toolForm
div class=toolFormTitleUsers informations/div
table
theadthUID/ththemail/th/thead
tbody
%for user in users:
tr
td${user['uid']}/td
td${user['email']}/td
td${user['key']}/td
td
form action=${h.url_for(
controller='userskeys', action='api_keys', cntrller=cntrller )}
method=POST
input type=hidden name=uid
value=${user['uid']} /
input type=submit name=new_api_key_button
value=Generate a new key now /
Re: [galaxy-dev] all the data files in .loc files needed to download ?
Hi everyone, Thank you very much for your help. I want to download the complete directory of galaxy data through rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX.But It can't work. And then I try to via http://dan.g2.bx.psu.edu/ by http://datacache.g2.bx.psu.edu/ ,I get 502 Bad Gateway. So what happens? How cat I get the data? Is there another way? Help me please. shenwiyn From: Carl Eberhard Date: 2013-02-27 22:28 To: Ross CC: shenwiyn; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello, Ross makes an important point: if this installation is for more than one user, you should install a more complete database system. This page may help with your decisions there: http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=showredirect=Admin%2FConfig%2FPerformance To your first question Is all the data in datacache.g2.bx.psu.edu/indexes needed?, I would say you should only need the data specific to the subject of your analyses and the tools you plan to use. To your second question can all of these needed data be downloaded (via rsync)? - perhaps you can clarify, please? We don't have any restriction on the amount you rsync from there and you're free to download all the data. If a problem or topic isn't covered in that wiki page, this mailing list is a good place to ask questions related to data set up. Thanks, Carl On Wed, Feb 27, 2013 at 5:44 AM, Ross ross.laza...@gmail.com wrote: Hi, shenwiyn I'd also add: Fourth, replace distributed default sqlite with postgresql to your list if it's for any serious use. Sqlite is ok for testing. On Wed, Feb 27, 2013 at 9:37 PM, shenwiyn shenw...@gmail.com wrote: Hello Carl, Thank you very much for your help.I have some thoughts about installing my local galaxy : First,download the latest source of galaxy from https://bitbucket.org/galaxy/galaxy-dist/ ,then install it in my local computer. Second,install dependencies tools mentioned in http://wiki.galaxyproject.org/Admin/Data%20Integration successfully. Third ,install the needed data and configure the .loc files from the following help of wiki page http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup. Finally ,our installation of local galaxy overs and it works in the mass.Is it right ? And I also have some confusions: First ,How large the total needed data is ?Is all the data in datacache.g2.bx.psu.edu/indexes needed ? Second, can all of these needed data be downloaded (via rsync) by the help of http://wiki.galaxyproject.org/Admin/Data%20Integration? These are the most important questions I concerned about now.I am so thankful for some of you advice. Thank you very much. shenwiyn From: Carl Eberhard Date: 2013-02-23 02:42 To: shenwiyn CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello shenwiyn, You may want to have a look at http://wiki.galaxyproject.org/Admin/Data%20Integration which provides more information specific to the indeces/data you'll need and how to install. Along with data management, that page has instructions on how to download (via rsync) the same data we use on our main server. It may be a good starting point. Thanks, Carl On Thu, Feb 21, 2013 at 8:58 PM, shenwiyn shenw...@foxmail.com wrote: Hi Carl Eberhard, Thank you very much for you help.I have another some questions : First, we need to install the needed data,for example sam_fa_indices.loc file of SAM Tools : index AaegL1 /afs/bx.psu.edu/depot/data/genome/AaegL1/sam_index/AaegL1.fa index AgamP3 /afs/bx.psu.edu/depot/data/genome/AgamP3/sam_index/AgamP3.fa index ailMel1 /afs/bx.psu.edu/depot/data/genome/ailMel1/sam_index/ailMel1.fa index anoCar2 /afs/bx.psu.edu/depot/data/genome/anoCar2/sam_index/anoCar2.fa index apiMel2 /afs/bx.psu.edu/depot/data/genome/apiMel2/sam_index/apiMel2.fa index apiMel3 /afs/bx.psu.edu/depot/data/genome/apiMel3/sam_index/apiMel3.fa index aplCal1 /afs/bx.psu.edu/depot/data/genome/aplCal1/sam_index/aplCal1.fa so we need to download AaegL1.fa,AgamP3.fa,ailMel1.fa,anoCar2.fa,apiMel2.fa,apiMel3.fa,and so on ,then install all of this needed datas to /afs/bx.psu.edu/depot/data/genome/aplCal1/sam_index/,is it right? Second, from the needed datas mentioned in the .loc files in http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup ,we need to download too much data,can we get all these data from some website instead of searching them on Iternet one by one? Thanks, shenwiyn From: Carl Eberhard Date: 2013-02-22 01:20 To: shenwiyn Subject: Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello, Yes a local galaxy requires a few steps in order to install the needed data. The following wiki page should help get you started: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Let me know if you need more information, Carl On Tue, Feb
Re: [galaxy-dev] Macs14 - Invalid Literal for int error
Hi Greg - the issue is that when the wrapper processes the Macs output, it attempts to turn the 2nd column of every non-comment line (the start field) into an integer (as an aside, it then also subtracts 1 from this value). Unfortunately the line starting chr start end ... isn't commented, so the integer conversion fails causing the error you saw. The patch just traps for the integer conversion error. HTH, best wishes, Peter On 27/02/13 19:16, greg wrote: Thanks Peter. I'm running it now after applying your fix. Any idea what the problem was? -Greg On Wed, Feb 27, 2013 at 4:21 AM, Peter Briggs peter.bri...@manchester.ac.uk wrote: Hello Greg It looks like you're running the version of the MACS14 tool from the toolshed? I think we also ran into this here and I patched the macs14_wrapper.py thusly to work around it: diff --git a/macs14/macs142_wrapper.py b/macs14/macs142_wrapper.py index ccefb10..c0cf099 100644 --- a/macs14/macs142_wrapper.py +++ b/macs14/macs142_wrapper.py @@ -37,7 +37,13 @@ def xls_to_interval( xls_file, interval_file, header = None ): else: fields = line.split( '\t' ) if len( fields ) 1: -fields[1] = str( int( fields[1] ) - 1 ) +try: +# Try to convert 'start' to int and shift +fields[1] = str( int( fields[1] ) - 1 ) +except ValueError: +# Integer conversion failed so comment out +# bad line instead +fields[0] = #%s % fields[0] out.write( '\t'.join( fields ) ) out.close() I'm intending to feed this back to the tool authors once things got a bit quieter here. HTH, best wishes Peter On 26/02/13 15:52, greg wrote: Hi guys, (Sorry for showing up on this list so much, hopefully I'll get everything running soon!) On our local galaxy install when I try to run MACS14 like this: http://snag.gy/RYBBN.jpg we get this error: Dataset generation errors Dataset 74: MACS14 on data 29 and data 24 (peaks: bed) Tool execution generated the following error message: Traceback (most recent call last): File /misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py, line 132, in module if __name__ == __main__: main() File /misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py, line 94, in main xls_to_interval( create_peak_xls_file, options['xls_to_interval']['peaks_file'], header = 'peaks file' ) File /misc/local/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/ryo-tas/macs14/cdd9791c0afa/macs14/macs14_wrapper.py, line 40, in xls_to_interval fields[1] = str( int( fields[1] ) - 1 ) ValueError: invalid literal for int() with base 10: 'start' ___ 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/ -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___ 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] purging datasets doesn't free up disk space
Hello, our Galaxy server is running low on disk space, so I asked all users to (permanently) delete old histories and datasets. One specific user alone managed to reduce his space usage by 2 TB. That's at least what the Galaxy server says. Afterwards I additionally ran the following scripts: delete_userless_histories.sh -d 1 -r -f purge_histories.sh -d 1 -r -f purge_libraries.sh -d 1 -r -f purge_folders.sh -d 1 -r -f python cleanup_datasets.py universe_wsgi.ini -d 200 -6 -r -f purge_datasets.sh -d 1 -r -f Purging the histories took very long (about a day) and the log of deleted histories is huge. Purging the datasets also took some time. However, my disk usage is still the same as before. It wasn't reduced at all. Did I miss some important step or some waiting time? Any help would be appreciated. Thanks, Sarah ___ 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/
Re: [galaxy-dev] bowtie-wrapper
Hmm, I don't see a patch for your changes to the wrapper script. Can you please bundle up and send along your tool definition + wrapper script changes and I'll add it to the card? Thanks, J. On Feb 28, 2013, at 4:47 AM, Peter Briggs wrote: Hi Jeremy - that's awesome, thanks! One thing: not sure if I read this right (I'm a Trello newbie) however it looks like only the patch to the tool XML has was attached to the card. This change also requires a patch to the python wrapper script (should have been attached to my earlier message). Apologies if I missed something, thanks again Best wishes, Peter On 27/02/13 18:33, Jeremy Goecks wrote: Thanks Peter. I've added your patch to the Trello card tracking incorporation of community contributions to the Bowtie wrapper: https://trello.com/c/TdYxdbkm Best, J. On Feb 27, 2013, at 4:35 AM, Peter Briggs wrote: Hello Alexander I've made some changes to our local copy of the bowtie tool files (bowtie_wrapper.xml and bowtie_wrapper.py) to give the option of capturing bowtie's stderr output and adding it as an additional history item (here the statistics in this output is used as input to a local tool). I've attached patches to the tool in case they're any use to you. (As an aside and more generally: I'm not sure how to manage these local customisations in the longer term - what do other people on this list do?) HTH, best wishes, Peter On 25/02/13 11:29, Alexander Kurze wrote: Hello, I am using the bowtie-wrapper on my locally installed galaxy server to align reads. However I missing the stats read-out. Is there any possibility to include statistics about unaligned reads? If I use bowtie vi comman line I get following output: bowtie ~/dm3 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam End-to-end 2/3-mismatch full-index search: 01:00:21 # reads processed: 12084153 # reads with at least one reported alignment: 9391748 (77.72%) # reads that failed to align: 2692405 (22.28%) Reported 30293838 alignments to 1 output stream(s) The output should be normally saved in the stderr but unfortunatly the stderr is somehow deleted after the alignment job is done in bowtie under galaxy. Any idea how I can still access the stats? Thanks, Alex -- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341 ___ 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/ -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 bowtie_wrapper.xml.patch -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___ 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/
Re: [galaxy-dev] purging datasets doesn't free up disk space
Hi Sarah May be the histories and/or datasets are shared with users who did not delete them? Also, have you looked at the log files? What is written in the log files for the purge_datasets.sh step? Do you have lines like: Removing disk, file ***/database/files/008/dataset_8271.dat and at the very end, something like: Purged 82 datasets Freed disk space: 647719608 Elapsed time: 1.51890397072 And I am confused with the way you call the scripts. This might be explained by different galaxy versions, however: delete_userless_histories.sh is in my case a wrapper executing 'cleanup_datasets.py' with the options: -d 90 -1. I do not provide the options when I call it. and the same is true for all the other scripts Regards, Hans-Rudolf On 02/28/2013 01:51 PM, Sarah Diehl wrote: Hello, our Galaxy server is running low on disk space, so I asked all users to (permanently) delete old histories and datasets. One specific user alone managed to reduce his space usage by 2 TB. That's at least what the Galaxy server says. Afterwards I additionally ran the following scripts: delete_userless_histories.sh -d 1 -r -f purge_histories.sh -d 1 -r -f purge_libraries.sh -d 1 -r -f purge_folders.sh -d 1 -r -f python cleanup_datasets.py universe_wsgi.ini -d 200 -6 -r -f purge_datasets.sh -d 1 -r -f Purging the histories took very long (about a day) and the log of deleted histories is huge. Purging the datasets also took some time. However, my disk usage is still the same as before. It wasn't reduced at all. Did I miss some important step or some waiting time? Any help would be appreciated. Thanks, Sarah ___ 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/ ___ 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/
Re: [galaxy-dev] access to api when using apache ldap auth
Hi Brad,
I think the method that Thon deBoer is using here is probably the best way to
do it:
http://dev.list.galaxyproject.org/Setting-up-a-proxy-with-authentication-while-waiving-this-for-API-calls-td4658497.html
--nate
On Feb 27, 2013, at 5:34 PM, Langhorst, Brad wrote:
I need to access the api using an api key…
Does anybody have a working apache configuration for that? A search at
galaxyproject.org/search didn't turn anything up.
I tried this: but that causes the history to fail to update.
Location /
Order allow,deny
allow from all
AuthType Basic
AuthName NEB Credentials
AuthBasicProvider ldap
AuthzLDAPAuthoritative off
AuthLDAPBindDN @
AuthLDAPBindPassword x
AuthLDAPURL ldap://host…?sAMAccountName
require valid-user
RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e
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
XSendFile on
XSendFileAllowAbove on
/Location
Location /api
Satisfy Any
Re: [galaxy-dev] purging datasets doesn't free up disk space
Hi Hans, thanks for your help. I didn't realize the sh scripts came with their own options. I just misunderstood that in the documentation. It seems to have worked though, the log file says: # 2013-02-28 11:56:20 - Handling stuff older than 1 days ... Purged 10097 datasets Freed disk space: 9515493164336 Elapsed time: 5669.43398285 So the freed disk space should be around 9 TB, right? Best regards, Sarah - Original Message - From: Hans-Rudolf Hotz h...@fmi.ch To: Sarah Diehl di...@ie-freiburg.mpg.de Cc: galaxy-dev@lists.bx.psu.edu List galaxy-dev@lists.bx.psu.edu Sent: Thursday, February 28, 2013 4:18:49 PM Subject: Re: [galaxy-dev] purging datasets doesn't free up disk space Hi Sarah May be the histories and/or datasets are shared with users who did not delete them? Also, have you looked at the log files? What is written in the log files for the purge_datasets.sh step? Do you have lines like: Removing disk, file ***/database/files/008/dataset_8271.dat and at the very end, something like: Purged 82 datasets Freed disk space: 647719608 Elapsed time: 1.51890397072 And I am confused with the way you call the scripts. This might be explained by different galaxy versions, however: delete_userless_histories.sh is in my case a wrapper executing 'cleanup_datasets.py' with the options: -d 90 -1. I do not provide the options when I call it. and the same is true for all the other scripts Regards, Hans-Rudolf On 02/28/2013 01:51 PM, Sarah Diehl wrote: Hello, our Galaxy server is running low on disk space, so I asked all users to (permanently) delete old histories and datasets. One specific user alone managed to reduce his space usage by 2 TB. That's at least what the Galaxy server says. Afterwards I additionally ran the following scripts: delete_userless_histories.sh -d 1 -r -f purge_histories.sh -d 1 -r -f purge_libraries.sh -d 1 -r -f purge_folders.sh -d 1 -r -f python cleanup_datasets.py universe_wsgi.ini -d 200 -6 -r -f purge_datasets.sh -d 1 -r -f Purging the histories took very long (about a day) and the log of deleted histories is huge. Purging the datasets also took some time. However, my disk usage is still the same as before. It wasn't reduced at all. Did I miss some important step or some waiting time? Any help would be appreciated. Thanks, Sarah ___ 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/ ___ 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/
Re: [galaxy-dev] purging datasets doesn't free up disk space
Ok, sorry for having bothered you again with my stupidness... I actually have a test instance of galaxy on the same server with the database directory hard-linked. After I deleted that one the space was free *d'oh*. - Original Message - From: Sarah Diehl di...@ie-freiburg.mpg.de To: Hans-Rudolf Hotz h...@fmi.ch, galaxy-dev@lists.bx.psu.edu List galaxy-dev@lists.bx.psu.edu Sent: Thursday, February 28, 2013 5:07:58 PM Subject: Re: [galaxy-dev] purging datasets doesn't free up disk space Hi Hans, thanks for your help. I didn't realize the sh scripts came with their own options. I just misunderstood that in the documentation. It seems to have worked though, the log file says: # 2013-02-28 11:56:20 - Handling stuff older than 1 days ... Purged 10097 datasets Freed disk space: 9515493164336 Elapsed time: 5669.43398285 So the freed disk space should be around 9 TB, right? Best regards, Sarah - Original Message - From: Hans-Rudolf Hotz h...@fmi.ch To: Sarah Diehl di...@ie-freiburg.mpg.de Cc: galaxy-dev@lists.bx.psu.edu List galaxy-dev@lists.bx.psu.edu Sent: Thursday, February 28, 2013 4:18:49 PM Subject: Re: [galaxy-dev] purging datasets doesn't free up disk space Hi Sarah May be the histories and/or datasets are shared with users who did not delete them? Also, have you looked at the log files? What is written in the log files for the purge_datasets.sh step? Do you have lines like: Removing disk, file ***/database/files/008/dataset_8271.dat and at the very end, something like: Purged 82 datasets Freed disk space: 647719608 Elapsed time: 1.51890397072 And I am confused with the way you call the scripts. This might be explained by different galaxy versions, however: delete_userless_histories.sh is in my case a wrapper executing 'cleanup_datasets.py' with the options: -d 90 -1. I do not provide the options when I call it. and the same is true for all the other scripts Regards, Hans-Rudolf On 02/28/2013 01:51 PM, Sarah Diehl wrote: Hello, our Galaxy server is running low on disk space, so I asked all users to (permanently) delete old histories and datasets. One specific user alone managed to reduce his space usage by 2 TB. That's at least what the Galaxy server says. Afterwards I additionally ran the following scripts: delete_userless_histories.sh -d 1 -r -f purge_histories.sh -d 1 -r -f purge_libraries.sh -d 1 -r -f purge_folders.sh -d 1 -r -f python cleanup_datasets.py universe_wsgi.ini -d 200 -6 -r -f purge_datasets.sh -d 1 -r -f Purging the histories took very long (about a day) and the log of deleted histories is huge. Purging the datasets also took some time. However, my disk usage is still the same as before. It wasn't reduced at all. Did I miss some important step or some waiting time? Any help would be appreciated. Thanks, Sarah ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] first install, MySQL date
On Feb 28, 2013, at 7:37 AM, Arnau Bria wrote: Hi all, my name is Arnau Bria and I work at CRG, in BCN. I'm a sysadmin and I'm helping one user to install/configure galaxy and to run jobs in our SGE cluster. I think this is the correct list for asking SGE/MySQL questions, if not, let me apology in advance. I have a question about MySQL dates. system date is correct and uses CET (I'm in Spain), MySQL i sconfigured to use system's timezone: date Thu Feb 28 13:38:10 CET 2013 SELECT @@global.time_zone, @@session.time_zone; ++-+ | @@global.time_zone | @@session.time_zone | ++-+ | SYSTEM | SYSTEM | ++-+ 1 row in set (0.02 sec) but SGE job dates are wrong: create_time 2013-02-28 12:37:48 notice it shows 12:37 and it should be 13:37. is this importatn? may I change glaxy's timezone in some way? Hi Arnau, The times are intentionally stored in the database in UTC. Times are rarely shown in the interface, but when they are, they should be properly adjusted using the system's currently set timezone. Thanks, --nate TIA, Arnau ___ 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/ ___ 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] blend4j
Hi all,
Is this the correct forum to post blend4j issues ? Apologies if this is not the
case.
I was trying to run a custom workflow via blend4j, according to
https://github.com/jmchilton/blend4j
In my hands, the call to workflowDetails.getInputs() returns an empty Map. I
believe the corresponding REST request looks like:
/galaxy/api/workflows/workflow id?key=API key
In the JSON response, the 'inputs' attribute is empty indeed ({url:
/galaxy/api/workflows/f09437b8822035f7, inputs: {}, ...).
I do not understand why this is the case because 2 steps require inputs to be
set at runtime. Via the Galaxy web interface those required parameters can be
set and the workflow is running smoothly.
Or has the term 'inputs' nothing to do with 'parameters' ?
Regards,
Marc
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Re: [galaxy-dev] bowtie-wrapper
Attached to the card, thanks Peter. J. On Feb 28, 2013, at 11:14 AM, Peter Briggs wrote: Hi Jeremy No problem - zip file with the two patches is attached, please let me know if there's a problem. Best wishes Peter On 28/02/13 15:07, Jeremy Goecks wrote: Hmm, I don't see a patch for your changes to the wrapper script. Can you please bundle up and send along your tool definition + wrapper script changes and I'll add it to the card? Thanks, J. On Feb 28, 2013, at 4:47 AM, Peter Briggs wrote: Hi Jeremy - that's awesome, thanks! One thing: not sure if I read this right (I'm a Trello newbie) however it looks like only the patch to the tool XML has was attached to the card. This change also requires a patch to the python wrapper script (should have been attached to my earlier message). Apologies if I missed something, thanks again Best wishes, Peter On 27/02/13 18:33, Jeremy Goecks wrote: Thanks Peter. I've added your patch to the Trello card tracking incorporation of community contributions to the Bowtie wrapper: https://trello.com/c/TdYxdbkm Best, J. On Feb 27, 2013, at 4:35 AM, Peter Briggs wrote: Hello Alexander I've made some changes to our local copy of the bowtie tool files (bowtie_wrapper.xml and bowtie_wrapper.py) to give the option of capturing bowtie's stderr output and adding it as an additional history item (here the statistics in this output is used as input to a local tool). I've attached patches to the tool in case they're any use to you. (As an aside and more generally: I'm not sure how to manage these local customisations in the longer term - what do other people on this list do?) HTH, best wishes, Peter On 25/02/13 11:29, Alexander Kurze wrote: Hello, I am using the bowtie-wrapper on my locally installed galaxy server to align reads. However I missing the stats read-out. Is there any possibility to include statistics about unaligned reads? If I use bowtie vi comman line I get following output: bowtie ~/dm3 -v 2 -k 5 --best --strata -S -t reads.fastq reads.sam End-to-end 2/3-mismatch full-index search: 01:00:21 # reads processed: 12084153 # reads with at least one reported alignment: 9391748 (77.72%) # reads that failed to align: 2692405 (22.28%) Reported 30293838 alignments to 1 output stream(s) The output should be normally saved in the stderr but unfortunatly the stderr is somehow deleted after the alignment job is done in bowtie under galaxy. Any idea how I can still access the stats? Thanks, Alex -- Alexander Kurze, DPhil University of Oxford Department of Biochemistry South Parks Road Oxford, OX1 3QU United Kingdom Tel: +44 1865 613 230 Fax:+44 1865 613 341 ___ 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/ -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 bowtie_wrapper.xml.patch -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 bowtie_wrapper_patches_pjbriggs.zip ___ 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/
Re: [galaxy-dev] blend4j
This is not a blend4j issue, it is more of a Galaxy API issue. I think
it is essentially a known problem that you cannot specify runtime
parameters for workflow, only data inputs. Here the relevant piece of
Galaxy code:
inputs = {}
for step in latest_workflow.steps:
if step.type == 'data_input':
inputs[step.id] = {'label':step.tool_inputs['name'], 'value':}
else:
pass
# Eventually, allow regular tool parameters to be
inserted and modified at runtime.
# p = step.get_required_parameters()
I think the meantime, the work around is not define these are workflow
parameters but instead hard code some values, and then pull down,
rewrite, and reupload a new workflow for each execution:
WorkflowsClient client = galaxyInstance.getWorkflowsClient();
String workflowJson = client.exportWorkflow(originalWorkflowId);
// modify workflow json
Workflow importedWorkflow = client.importWorkflow(workflowJson);
String importedWorkflowId = importedWorkflow.getId();
It is not pretty obviously. They are pretty good about responding to
API pull requests so if you have the time to fix the Galaxy code
itself I think everyone would appreciate that fix.
-John
On Thu, Feb 28, 2013 at 3:24 PM, Marc Logghe marc.log...@ablynx.com wrote:
Hi all,
Is this the correct forum to post blend4j issues ? Apologies if this is not
the case.
I was trying to run a custom workflow via blend4j, according to
https://github.com/jmchilton/blend4j
In my hands, the call to workflowDetails.getInputs() returns an empty Map. I
believe the corresponding REST request looks like:
/galaxy/api/workflows/workflow id?key=API key
In the JSON response, the ‘inputs’ attribute is empty indeed ({url:
/galaxy/api/workflows/f09437b8822035f7, inputs: {}, …).
I do not understand why this is the case because 2 steps require inputs to
be set at runtime. Via the Galaxy web interface those required parameters
can be set and the workflow is running smoothly.
Or has the term ‘inputs’ nothing to do with ‘parameters’ ?
Regards,
Marc
THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY
TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED,
CONFIDENTIAL AND EXEMPT FROM DISCLOSURE.
If the reader of this E-mail message is not the intended recipient, you are
hereby notified that any dissemination, distribution or copying of this
communication is strictly prohibited. If you have received this
communication in error, please notify us immediately at abl...@ablynx.com.
Thank you for your co-operation.
NANOBODY and NANOCLONE are registered trademarks of Ablynx N.V.
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___
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Re: [galaxy-dev] blend4j
-Original Message-
From: jmchil...@gmail.com [mailto:jmchil...@gmail.com] On Behalf Of John Chilton
Sent: Thursday, February 28, 2013 11:27 PM
To: Marc Logghe
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] blend4j
This is not a blend4j issue, it is more of a Galaxy API issue. I think
it is essentially a known problem that you cannot specify runtime
parameters for workflow, only data inputs. Here the relevant piece of
Galaxy code:
inputs = {}
for step in latest_workflow.steps:
if step.type == 'data_input':
inputs[step.id] = {'label':step.tool_inputs['name'], 'value':}
else:
pass
# Eventually, allow regular tool parameters to be
inserted and modified at runtime.
# p = step.get_required_parameters()
I think the meantime, the work around is not define these are workflow
parameters but instead hard code some values, and then pull down,
rewrite, and reupload a new workflow for each execution:
WorkflowsClient client = galaxyInstance.getWorkflowsClient();
String workflowJson = client.exportWorkflow(originalWorkflowId);
// modify workflow json
Workflow importedWorkflow = client.importWorkflow(workflowJson);
String importedWorkflowId = importedWorkflow.getId();
It is not pretty obviously. They are pretty good about responding to
API pull requests so if you have the time to fix the Galaxy code
itself I think everyone would appreciate that fix.
-John
Hi John
Thanks for the quick answer; I'll give it a try.
Regarding the fix: you need to give me some time, started with a python
tutorial only 2 days ago ;-)
Regards,
Marc
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[galaxy-dev] cleanup script fails on dataset_instance None
Hi,I have some problems with the cleanup scripts...I seem to have a dataset_instance that is "None" and if it tries to delete that you obviously get an error. (See below..I added the print statement, but the line is the same)...I wonder how I could get a dataset with a None definition and how can I clean up the database for this?Thanks,Thonsh purge_libraries.shTraceback (most recent call last): File "./scripts/cleanup_datasets/cleanup_datasets.py", line 527, in module if __name__ == "__main__": main() File "./scripts/cleanup_datasets/cleanup_datasets.py", line 122, in main purge_libraries( app, cutoff_time, options.remove_from_disk, info_only = options.info_only, force_retry = options.force_retry ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 217, in purge_libraries _purge_folder( library.root_folder, app, remove_from_disk, info_only = info_only ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 500, in _purge_folder _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 500, in _purge_folder _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 500, in _purge_folder _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) File "./scripts/cleanup_datasets/cleanup_datasets.py", line 498, in _purge_folder _purge_dataset_instance( ldda, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable File "./scripts/cleanup_datasets/cleanup_datasets.py", line 376, in _purge_dataset_instance print('dataset_instance.id: {0}'.format(dataset_instance.id))AttributeError: 'NoneType' object has no attribute 'id'(galaxy_env)[svcgalaxy@srv151 cleanup_datasets]$ sh purge_libraries.sh___
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[galaxy-dev] Coming soon: BOSC/Broad Hackathon, SciPy Bioinformatics, BOSC Codefest
Hi all; There are some upcoming coding events and conferences of interest to open source biology programmers: - BOSC/Broad Interoperability Hackathon -- This is a two day coding session at the Broad Institute in Cambridge, MA on April 7-8 focused on improving tool interoperability. Sign up and details: http://j.mp/XJT6ew - SciPy 2013 -- The Scientific Python conference is June 26-27 in Austin and has a Bioinformatics mini-symposia this year. They're doing some great work like IPython, NumPy, SciPy and scikit-learn; and this is a nice opportunity to reach a new set of like minded programmers and expand the open source bioinformatics community. Bioinformatics mini-symposia: http://j.mp/Z4xxXB Abstract details: http://conference.scipy.org/scipy2013/about.php - Codefest at the Bioinformatics Open Source Conference -- This year BOSC is taking place in Berlin from July 19-20 and we'll have a two day coding session before the conference. This is the 4th year of Codefests and they've proven to be a productive and fun time to work collectively on open source projects. Sign up and details: http://www.open-bio.org/wiki/Codefest_2013 BOSC conference: http://www.open-bio.org/wiki/BOSC_2013 Here are the key dates for the events and abstracts: March 20, 2013: SciPy abstracts due April 7-8, 2013: BOSC/Broad Interoperability Hackathon, Cambridge, MA April 12, 2013: BOSC abstracts due June 24-29, 2013: SciPy in Austin, TX July 17-18, 2013: Codefest 2013, Berlin July 19-20, 2013: BOSC 2013, Berlin Looking forward to seeing everyone this spring and summer for plenty of fun science and code, Brad ___ 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] Error on the sandbox toolshed when updating files
Hi - I was only trying to upload a new gzipped-tarfile with new files to a repository that I own on the sandbox toolshed server, and get the following error: Server ErrorURL: http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d Module paste.exceptions.errormiddleware:*144* in __call__ http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d# app_iter *=* self*.*application*(*environ*,* sr_checker*)* Module paste.debug.prints:*106* in __call__ http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d# environ*,* self*.*app*)* Module paste.wsgilib:*543* in intercept_output http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d# app_iter *=* application*(*environ*,* replacement_start_response*)* Module paste.recursive:*84* in __call__ http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d# *return* self*.*application*(*environ*,* start_response*)* Module paste.httpexceptions:*633* in __call__ http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d# *return* self*.*application*(*environ*,* start_response*)* Module galaxy.web.framework.base:*128* in __call__ http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d# *return* self*.*handle_request*(* environ*,* start_response *)* Module galaxy.web.framework.base:*184* in handle_request http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d# body *=* method*(* trans*,* kwargs *)* Module galaxy.web.framework:*94* in decorator http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d# *return* func*(* self*,* trans*,* ***args*,* kwargs *)* Module galaxy.webapps.tool_shed.controllers.upload:*108* in upload http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d# self*.*upload_tar*(* trans*,* repository*,* tar*,* uploaded_file*,* upload_point*,* remove_repo_files_not_in_tar*,* commit_message*,* new_repo_alert *)* Module galaxy.webapps.tool_shed.controllers.upload:*283* in upload_tar http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d# *return* self*.*__handle_directory_changes*(*trans*,* repository*,* full_path*,* filenames_in_archive*,* remove_repo_files_not_in_tar*,* new_repo_alert*,* commit_message*,* undesirable_dirs_removed*,* undesirable_files_removed*)* Module galaxy.webapps.tool_shed.controllers.upload:*345* in __handle_directory_changes http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d# commands*.*commit*(* repo*.*ui*,* repo*,* full_path*,* user*=*trans*.*user*. *username*,* message*=*commit_message *)* Module mercurial.commands:*1279* in commit http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d# node *=* cmdutil*.*commit*(*ui*,* repo*,* commitfunc*,* pats*,* opts*)* Module mercurial.cmdutil:*1294* in commit http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d# scmutil*.*match*(*repo*[*None*]**,* pats*,* opts*)**,* opts*)* Module mercurial.commands:*1277* in commitfunc http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d# match*,* editor*=*e*,* extra*=*extra*)* Module mercurial.localrepo:*1199* in commit http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d# ret *=* self*.*commitctx*(*cctx*,* True*)* Module mercurial.localrepo:*1270* in commitctx http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d# p2*.*manifestnode*(**)**,* *(*new*,* drop*)**)* Module mercurial.manifest:*197* in add http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d# cachedelta *=* *(*self*.*rev*(*p1*)**,* addlistdelta*(*addlist*,* delta*)**) * Module mercurial.manifest:*124* in addlistdelta http://testtoolshed.g2.bx.psu.edu/upload/upload?repository_id=f5109f746542d96d# addlist*[*start*:*end*]* *=* array*.*array*(*'c'*,* content*)* *TypeError: array item must be char* Is there a better way to upload updated files to those repositories? -- Peter Waltman, Ph.D. pwalt...@ucsc.edu 617.347.187 ___ 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] March 2013 Galaxy Update
Hello all, The March 2013 Galaxy Update is now availablehttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03. See http://wiki.galaxyproject.org/GalaxyUpdates/2013_03. *Highlights include:* - *GCC2013 http://wiki.galaxyproject.org/GalaxyUpdates/2013_03#GCC2013 early registration http://wiki.galaxyproject.org/Events/GCC2013/Register, and oral presentation and poster abstract submissionhttp://wiki.galaxyproject.org/Events/GCC2013/Abstracts are now open*, and we have several new sponsorshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03#Sponsorships ! - The March 20 GalaxyAdmins meetuphttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03#March_GalaxyAdmins_Web_Meetup will feature Hailiang (Leon) Mei, and David van Enckevort speaking on *NBIC Galaxy http://galaxy.nbic.nl/ at SURFsara's HPC cloudhttps://www.surfsara.nl/ * - A new public Galaxy serverhttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03#New_Public_Galaxy_Servers in Costa Rica - New papershttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03#New_Papers - Open Positionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03#Who.27s_Hiring at four different institutions - Other Upcoming Events and Deadlineshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03#Other_Upcoming_Events_and_Deadlines - Galaxy Distributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03#Galaxy_Distributions - Tool Shed Contributionshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03#Tool_Shed_Contributions - Other Newshttp://wiki.galaxyproject.org/GalaxyUpdates/2013_03#Other_News If you have anything you would like to see in the April *Galaxy Updatehttp://wiki.galaxyproject.org/GalaxyUpdates *, please let us know. Thanks, Dave C -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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] Error when upgrading the database to version 110
Hi guys, I was given the following error when upgrading the database from 109 to 110: 0109_add_repository_dependency_tables DEBUG 2013-03-01 15:14:15,554 Creating repository_repository_dependency_association table failed: (OperationalError) (1059, Identifier name 'ix_repository_repository_dependency_association_tool_shed_repository_id' is too long) u'CREATE INDEX ix_repository_repository_dependency_association_tool_shed_repository_id ON repository_repository_dependency_association (tool_shed_repository_id)' () 0109_add_repository_dependency_tables DEBUG 2013-03-01 15:14:15,554 Creating repository_repository_dependency_association table failed: (OperationalError) (1059, Identifier name 'ix_repository_repository_dependency_association_tool_shed_repository_id' is too long) u'CREATE INDEX ix_repository_repository_dependency_association_tool_shed_repository_id ON repository_repository_dependency_association (tool_shed_repository_id)' () So I guess the indexes weren't created. I am using MySQL, is it a big deal for Galaxy? Cheers, Derrick ___ 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/
Re: [galaxy-dev] Problem installing Deseq from toolshed
Still waiting on a reply! Any suggestion is appreciated. On Tue, Feb 26, 2013 at 1:55 PM, Mahtab Mirmomeni m.mirmom...@student.unimelb.edu.au wrote: Hi all, I have installed Deseq (by vipints) from the main galaxy toolshed and have followed the make instructions but I'm still not unable to run it inside Galaxy and I get the following error. (Path is the path to our local galaxy instance) error: get_read_counts: Path/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/2b3bb3348076/deseq_hts/deseq-hts_1.0/mex/get_reads.mex: failed to load: /mnt/all/cloudman/galaxy/clare/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/2b3bb3348076/deseq_hts/deseq-hts_1.0/mex/get_reads.mex: undefined symbol: bam_index_destroy error: called from: error: Path/shed_tools/toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/2b3bb3348076/deseq_hts/deseq-hts_1.0/src/get_read_counts.m at line 97, column 34 starting Octave failed I should add that I can run octave from command line and it seems to be working. Any suggestions is much appreciated. Thanks Mahtab ___ 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] Error while installing DESeq-hts
Hi, I have tried to follow instructions provided with this installation a) Run ./setup_deseq-hts.sh and setup paths and configuration options for DESeq-hts. I successfully ran the setup scrip but is there other path and conf that need to be done apart from those done by this script ? b) Inside the mex folder execute the make file to create platform dependent .mex files cd mex/Makefile make [interpreter] make octave for octave make matlab for matlab make all for octave and matlab When I run make octave I get the following error message : /usr/bin/mkoctfile -g --mex get_reads.cpp get_reads_direct.cpp mex_input.cpp read.cpp -I/mnt/galaxyTools/tools/samtools/0.1.16 -L/mnt/galaxyTools/tools/samtools/0.1.16 -lbam -lz -lcurses get_reads_direct.cpp:14:17: fatal error: sam.h: No such file or directory compilation terminated. make: *** [get_reads.mex] Error 1 It feels like this is link to samtools, when browsing on the web I found information about SAMTOOLS_ROOT env variable but changing this one doesn't solve my problem. As anyone else encounter this kind of things ? Regards, Philippe ___ 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/
Re: [galaxy-dev] Error while installing DESeq-hts
Hi Philipe Look into the bin/deseq_config.sh and see if the path to octave and samtools have been set correctly. I'm having problem running DESeq too. I go past this point by I get get_reads.mex error: path/shed_tools/ toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/2b3bb3348076/deseq_hts/deseq-hts_1.0/mex/get_reads.mex: failed to load: /mnt/all/cloudman/galaxy/ clare/shed_tools/ toolshed.g2.bx.psu.edu/repos/vipints/deseq_hts/2b3bb3348076/deseq_hts/deseq-hts_1.0/mex/get_reads.mex: undefined symbol: bam_index_destroy error when trying to run get_reads.mex in octave. Mahtab On Fri, Mar 1, 2013 at 3:54 PM, Philipe Moncuquet philippe.m...@gmail.comwrote: Hi, I have tried to follow instructions provided with this installation a) Run ./setup_deseq-hts.sh and setup paths and configuration options for DESeq-hts. I successfully ran the setup scrip but is there other path and conf that need to be done apart from those done by this script ? b) Inside the mex folder execute the make file to create platform dependent .mex files cd mex/Makefile make [interpreter] make octave for octave make matlab for matlab make all for octave and matlab When I run make octave I get the following error message : /usr/bin/mkoctfile -g --mex get_reads.cpp get_reads_direct.cpp mex_input.cpp read.cpp -I/mnt/galaxyTools/tools/samtools/0.1.16 -L/mnt/galaxyTools/tools/samtools/0.1.16 -lbam -lz -lcurses get_reads_direct.cpp:14:17: fatal error: sam.h: No such file or directory compilation terminated. make: *** [get_reads.mex] Error 1 It feels like this is link to samtools, when browsing on the web I found information about SAMTOOLS_ROOT env variable but changing this one doesn't solve my problem. As anyone else encounter this kind of things ? Regards, Philippe ___ 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/ ___ 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/
