[galaxy-dev] ActiveDirectory issues with auto register functionality

[Yves Gagnon]

Hello everybody!

I try to configure Active Directory authentication on our local instance.  So 
far, I got the authentication to work using direct binding.  I have these 
options in the auth_conf.xml :

No
Yes
ldap:/REDACTED /
{username}@REDACTED
{password}
False
{sAMAccountName}
True
{mail}

Paster.log:
galaxy.auth.providers.ldap_ad DEBUG 2015-09-03 11:26:20,158 LDAP authenticate: 
whoami is u:REDACTED\GagnonY
galaxy.auth.providers.ldap_ad DEBUG 2015-09-03 11:26:20,159 LDAP authentication 
successful

However, the authentication module does not seem to be able to fetch 
information from LDAP to auto register
With these settings, I get the debug message in galaxy when I try to log in :

URL: http://localhost:8080/user/login?use_panels=False
File 
'/home/galaxy/galaxy_app/galaxy/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py',
 line 364 in respond
  app_iter = self.application(environ, detect_start_response)
File 
'/home/galaxy/galaxy_app/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py',
 line 84 in __call__
  return self.application(environ, start_response)
File 
'/home/galaxy/galaxy_app/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py',
 line 633 in __call__
  return self.application(environ, start_response)
File '/home/galaxy/galaxy_app/galaxy/lib/galaxy/web/framework/base.py', line 
133 in __call__
  return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy_app/galaxy/lib/galaxy/web/framework/base.py', line 
191 in handle_request
  body = method( trans, **kwargs )
File 
'/home/galaxy/galaxy_app/galaxy/lib/galaxy/webapps/galaxy/controllers/user.py', 
line 482 in login
  message, status, user, success = self.__validate_login( trans, **kwd )
File 
'/home/galaxy/galaxy_app/galaxy/lib/galaxy/webapps/galaxy/controllers/user.py', 
line 524 in __validate_login
  autoreg = trans.app.auth_manager.check_auto_registration(trans, login, 
password)
File '/home/galaxy/galaxy_app/galaxy/lib/galaxy/auth/__init__.py', line 100 in 
check_auto_registration
  auth_result, auto_email, auto_username = provider.authenticate(email, 
username, password, options)
File '/home/galaxy/galaxy_app/galaxy/lib/galaxy/auth/providers/ldap_ad.py', 
line 177 in authenticate
  _get_subs(options, 'auto-register-email', params),
File '/home/galaxy/galaxy_app/galaxy/lib/galaxy/auth/providers/ldap_ad.py', 
line 19 in _get_subs
  return str(d[k]).format(**params)
KeyError: 'mail'

So for some reason, the module cannot fetch the mail field from AD.  If I try 
to bypass this by putting a harcoded email, same issue occurs with 
sAMAccountName field.  Did anybody encounter this before?

Thanks in advance for the help.

Yves Gagnon

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[galaxy-dev] July 2015 Galaxy Release (v 15.07)

[Martin Čech]

The very-slightly-delayed July 2015 Galaxy Release is out!
Full release notes:
http://galaxy.readthedocs.org/en/master/releases/15.07_announce.html

Highlights
 * *Interactive Environments* - The interactive environments (IE) framework
features several updates this release and Galaxy is now distributed with a
new IE for RStudio implemented by Eric Rasche.
 * *Workflow Editor Enhancements*  - The workflow editor has been
significantly revamped - it now uses newer tool form components and allow
construction of workflows with tools explicitly producing output
collections.
 * *Policies for Committers and Pull Requests*  - The process for adding
committers to the project and fielding pull requests has been formalized
and documented in the source code. Three new committers have been added to
the project - Björn Grüning, Nicola Soranzo, and Eric Rasche.
*Thank you for using Galaxy! *
The Galaxy Team
https://wiki.galaxyproject.org/GalaxyTeam
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Re: [galaxy-dev] LDAP Auto register - "username is None"

[Nicola Soranzo]

Hi Martin,
that's exactly what I was suggesting in my last email, sorry for not 
explaining myself better with a complete example!


I'm happy it's working for you now, I will create a PR to update the 
sample file example.


Thanks,
Nicola

On 03/09/15 12:47, Martin Vickers wrote:


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi,

Okay I've solved it. The issue was that a) (mail={email}) is all that 
is required in the search filter (to allow non-registered users) b) to 
return cn and mail in the search-fields for use with the 
auto-register-username and email. Finally, ensure auto-register is set 
to True.


True
ldaps://dc1.example.com
ou=Person,dc=dc1,dc=example,dc=com
cn=searchuser,ou=Person,dc=dc1,dc=example,dc=com
searchpassword
cn,mail
(mail={email})
False
{dn}
{password}
{cn}
{mail}

Cheers,

Martin

On 09/03/2015 11:59 AM, Martin Vickers wrote:
> Hi Nicola, > > So I've realised that none of that was actually the issue. The 
(&(uid={username})(mail={email})) part does work fine, it's the 
setting of the username that is the issue.  When the first 
unregistered user logs in, it works fine but the username is set to 
-10. When a second unregistered user attempts to login, they can't. If 
I manually change their username, the second user is then able to log 
in and once again the username is set to -10. (see attached images). > 
> I think the issue here stems from; > > 
{uid} > > since I 
don't have a uid property in our ldap server. I've tried all 
combinations of auto-register (True/False) and allow-register 
(True/False/Challenge) and haven't been able to get it to work. It 
also appears that auto-register-username and auto-register-email are 
requirements to use this authenticator as without it noone can log in 
(including registered users), and I get the following "Internal Server 
Error" message. > > This is my current auth_config.xml file; > 
>  > ldap > 
True > 
ldaps://dc1.example.com > 
ou=Person,dc=dc1,dc=example,dc=com > 
cn=searchuser,ou=Person,dc=dc1,dc=example,dc=com 
> searchpasssword > 
uid,mail > 
((mail={email})(uid={username})) 
> False > 
{dn} > 
{password} > 
{uid} > 
{mail} > 
 >  > > Doesn't one of the 
allow-register settings make/ask the user to provide a username rather 
than trying to auto generate it? or, is there a way to get the 
username out of the ldap server if it's not using uid to store it? > > 
Many thanks, > > Martin > > On 09/02/2015 06:09 PM, Nicola Soranzo 
wrote: > > Hi Martin, > > I suspect there's an error in the sample 
auth_conf.xml file,  should try to match only the 
email, not the username (unless you specify 
True, in which case it's 
viceversa) because it is not known when you first login. In fact, for 
ActiveDirectory the filter is: 
((objectClass=user)(mail={email})) 
So, can you try to change: 
((cn={username})(mail={email})) to 
something like: > > (mail={email}) 
Cheers, Nicola > > On 02/09/15 15:51, Martin Vickers wrote: > >> >> Hi 
Nicola, >> >> It's an OpenLDAP server. uid isn't set on ours, it's cn 
instead, so using ldapsearch I can correctly bind; >> >> dn: 
cn=mjv08,ou=Person,dc=dc1,dc=example,dc=com >> objectClass: aberPerson 
>> cn: mjv08 >> >> So authentication to the ldap server is working, 
the issue seems to be that when it's an unknown user, it's passing the 
following search string; >> >> 
(&(cn=None)(mail=unknownu...@aber.ac.uk)) >> >> rather than; >> >> 
(&(cn=unknownuser)(mail=unknownu...@aber.ac.uk)) >> >> hence the; >> 
>> galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 15:40:07,322 LDAP 
authenticate: username is None >> galaxy.auth.providers.ldap_ad 
WARNING 2015-09-02 15:40:07,485 LDAP authenticate: search returned no 
results >> >> How is {username} in auth_config.xml set? Does it parse 
{email} to get it? >> >> Many thanks, >> >> Martin >> >> On 09/02/2015 
03:38 PM, Nicola Soranzo wrote: >> > Hi Martin, > what LDAP server are 
you using? We have tested only OpenLDAP and > ActiveDirectory, but 
should work on any LDAP server. > > If it is OpenLDAP, I think you 
should use: > > uid,mail > 
((mail={email})(uid={username})) > 
{uid} > > More 
details in: > > 
https://github.com/galaxyproject/galaxy/blob/dev/config/auth_conf.xml.sample 
> > Cheers, > Nicola > > Il 02.09.2015 15:03 Martin Vickers ha 
scritto: > > Hi All, > > I've been trying to get the new LDAP module 
to work. It works fine for > existing users but I can't get 
auto-register to work. In the logs I can > see the successful logins 
look like this; > > galaxy.webapps.galaxy.controllers.user DEBUG 
2015-09-02 13:35:06,130 > trans.app.config.auth_config_file: 
./config/auth_conf.xml > galaxy.auth.providers.ldap_ad DEBUG 
2015-09-02 13:35:06,131 LDAP > authenticate: email is mj...@aber.ac.uk 
[1] > galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 13:35:06,131 LDAP 
> authenticate: username is mjv08 >  > 
galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 

[galaxy-dev] planemo and tool dependencies

[Steve Cassidy]

Hi all,
  I'm trying to test some tools under planemo and can't find out how to
have it install tool dependencies while setting up the environment.

The dependency is on a particular python module and we have a
tool_dependencies.xml file to describe it. I can't see a way to tell
planemo serve etc to refer to that file to get the dependencies.

Any help appreciated.

Steve

-- 
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy/
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Re: [galaxy-dev] planemo and tool dependencies

[Christian Brenninkmeijer]

Hi,

I wrote an extension that will help planemo pull in tool dependencies.

See 
https://github.com/galaxyproject/galaxy/blob/master/lib/galaxy/tools/deps/resolvers/unlinked_tool_shed_packages.py

It is for when the dependency was installed into galaxy but where planemo is 
not using the database to find that tool.

It works my helping planemo guess where the tool dependency may be.

Hope that helps.
Christian
University of Manchester

From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Steve Cassidy [steve.cass...@mq.edu.au]
Sent: Thursday, September 03, 2015 9:00 AM
To: galaxy-dev@lists.galaxyproject.org
Subject: [galaxy-dev] planemo and tool dependencies

Hi all,
  I'm trying to test some tools under planemo and can't find out how to have it 
install tool dependencies while setting up the environment.

The dependency is on a particular python module and we have a 
tool_dependencies.xml file to describe it. I can't see a way to tell planemo 
serve etc to refer to that file to get the dependencies.

Any help appreciated.

Steve

--
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy/
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Re: [galaxy-dev] Installing Cairo into Gakaxy

[Christian Brenninkmeijer]

In the continued effort to track down the issue of installing cairo into R

I found a bug in 
https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_1_2/41f43a2064ba
which installs 
https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.1.2-Linux-x84_64.tgz

This has hard code paths in it.
For example lib//pkgconfig/cairo.pc
prefix=/galaxy/builds/Linux-x86_64/install_dir

This is then picked up by cairo's configure script resulting in cairo not being 
found as it s clearly not where galaxy said it is!

Debugging continue!

Christian
University of Manchester




From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Christian Brenninkmeijer [christian.brenninkmei...@manchester.ac.uk]
Sent: Wednesday, September 02, 2015 11:40 AM
To: Björn Grüning; galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

I am still having issues installing Cairo into R

I have tracked part of the problem down to:
https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.1-Linux-x86_64.tgz 
does have any include files so no headers.

https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_2_1/3d28600fc82c has:
$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig
$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig

The set_to overwrites any environment_variable PKG_CONFIG values set by other 
packages

I changed the PKG_CONFIG setting to prepend to previous values and got:

checking cairo.h usability... yes
checking cairo.h presence... yes
checking for cairo.h... yes
checking for PNG support in Cairo... yes
install_environment.STDOUT DEBUG 2015-09-02 11:27:12,315 configure: 
CAIRO_LIBS=-L/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib
 
-L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib
 
-L/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib
 -lfreetype -lpng16 -lz -lcairo
checking for ATS font support in Cairo... no
configure: 
CAIRO_LIBS=-L/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib
 
-L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib
 
-L/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib
 -lfreetype -lpng16 -lz -lcairo
checking for library containing deflate... none required
install_environment.STDOUT DEBUG 2015-09-02 11:27:12,426 checking whether Cairo 
programs can be compiled... yes
checking whether Cairo programs can be compiled... yes
checking whether cairo_image_surface_get_format is declared... no
install_environment.STDOUT DEBUG 2015-09-02 11:27:12,499 checking for FreeType 
support in cairo... yes
install_environment.STDOUT DEBUG 2015-09-02 11:27:12,576 checking whether 
pkg-config knows about fontconfig or freetype2... yes
checking for FreeType support in cairo... yes
checking whether FreeType needs additional flags... yes
checking whether pkg-config knows about fontconfig or freetype2... yes
checking whether additional flags work... no
configure: error: Cannot use cairo-ft backend, although cairo claims it is 
working. Please check your caito installation and/or update cairo if necessary 
or set CAIRO_CFLAGS/CAIRO_LIBS accordingly.
ERROR: configuration failed for package ‘Cairo’


For the record the full cmd to setup R is:
PATH=/home/christian/galaxy/dependency_dir/pixman/0.32.4/iuc/package_pixman_0_32_4/873f53f1abcd/bin:$PATH;
 export PATH
PIXMAN_LIB_PATH=/home/christian/galaxy/dependency_dir/pixman/0.32.4/iuc/package_pixman_0_32_4/873f53f1abcd/lib;
 export PIXMAN_LIB_PATH
PKG_CONFIG_PATH=/home/christian/galaxy/dependency_dir/pixman/0.32.4/iuc/package_pixman_0_32_4/873f53f1abcd/lib/pkgconfig:$PKG_CONFIG_PATH;
 export PKG_CONFIG_PATH
PATH=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/bin:$PATH;
 export PATH
LIBPNG_ROOT=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6;
 export LIBPNG_ROOT
LIBPNG_LIB_PATH=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib;
 export LIBPNG_LIB_PATH
LIBPNG_INCLUDE_PATH=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/include;
 export LIBPNG_INCLUDE_PATH
LD_LIBRARY_PATH=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib:$LD_LIBRARY_PATH;
 export LD_LIBRARY_PATH
PKG_CONFIG_PATH=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib/pkgconfig:$PKG_CONFIG_PATH;
 export PKG_CONFIG_PATH
FREETYPE_LIB_PATH=/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib;
 export FREETYPE_LIB_PATH

Re: [galaxy-dev] LDAP Auto register - "username is None"

[Martin Vickers]

Hi Nicola,

So I've realised that none of that was actually the issue. The
(&(uid={username})(mail={email})) part does work fine, it's the setting
of the username that is the issue.  When the first unregistered user
logs in, it works fine but the username is set to -10. When a second
unregistered user attempts to login, they can't. If I manually change
their username, the second user is then able to log in and once again
the username is set to -10. (see attached images).

I think the issue here stems from;

{uid}

since I don't have a uid property in our ldap server. I've tried all
combinations of auto-register (True/False) and allow-register
(True/False/Challenge) and haven't been able to get it to work. It also
appears that auto-register-username and auto-register-email are
requirements to use this authenticator as without it noone can log in
(including registered users), and I get the following "Internal Server
Error" message.

This is my current auth_config.xml file;


ldap
True
ldaps://dc1.example.com
   
ou=Person,dc=dc1,dc=example,dc=com
   
cn=searchuser,ou=Person,dc=dc1,dc=example,dc=com
searchpasssword
uid,mail
   
((mail={email})(uid={username}))
False
{dn}
{password}
   
{uid}
{mail}



Doesn't one of the allow-register settings make/ask the user to provide
a username rather than trying to auto generate it? or, is there a way to
get the username out of the ldap server if it's not using uid to store it?

Many thanks,

Martin

On 09/02/2015 06:09 PM, Nicola Soranzo wrote:
> Hi Martin,
> I suspect there's an error in the sample auth_conf.xml file,
 should try to match only the email, not the username
(unless you specify True, in
which case it's viceversa) because it is not known when you first login.
In fact, for ActiveDirectory the filter is:
((objectClass=user)(mail={email}))
So, can you try to change:
((cn={username})(mail={email})) to
something like:
> (mail={email}) Cheers, Nicola
> On 02/09/15 15:51, Martin Vickers wrote:
>>
> Hi Nicola,
>
> It's an OpenLDAP server. uid isn't set on ours, it's cn instead, so
> using ldapsearch I can correctly bind;
>
> dn: cn=mjv08,ou=Person,dc=dc1,dc=example,dc=com
> objectClass: aberPerson
> cn: mjv08
>
> So authentication to the ldap server is working, the issue seems to be
> that when it's an unknown user, it's passing the following search string;
>
> (&(cn=None)(mail=unknownu...@aber.ac.uk))
>
> rather than;
>
> (&(cn=unknownuser)(mail=unknownu...@aber.ac.uk))
>
> hence the;
>
> galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 15:40:07,322 LDAP
> authenticate: username is None
> galaxy.auth.providers.ldap_ad WARNING 2015-09-02 15:40:07,485 LDAP
> authenticate: search returned no results
>
> How is {username} in auth_config.xml set? Does it parse {email} to get it?
>
> Many thanks,
>
> Martin
>
> On 09/02/2015 03:38 PM, Nicola Soranzo wrote:
> > Hi Martin, > what LDAP server are you using? We have tested only
> OpenLDAP and > ActiveDirectory, but should work on any LDAP server. >
> > If it is OpenLDAP, I think you should use: > >
> uid,mail >
> ((mail={email})(uid={username})) >
> {uid} > > More
> details in: > >
> https://github.com/galaxyproject/galaxy/blob/dev/config/auth_conf.xml.sample
> > > Cheers, > Nicola > > Il 02.09.2015 15:03 Martin Vickers ha
> scritto: > > Hi All, > > I've been trying to get the new LDAP module
> to work. It works fine for > existing users but I can't get
> auto-register to work. In the logs I can > see the successful logins
> look like this; > > galaxy.webapps.galaxy.controllers.user DEBUG
> 2015-09-02 13:35:06,130 > trans.app.config.auth_config_file:
> ./config/auth_conf.xml > galaxy.auth.providers.ldap_ad DEBUG
> 2015-09-02 13:35:06,131 LDAP > authenticate: email is mj...@aber.ac.uk
> [1] > galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 13:35:06,131 LDAP
> > authenticate: username is mjv08 >  >
> galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 13:35:06,235 LDAP >
> authentication successful > > and those that are unsuccessful have a
> username as None, which is why > the search filter isn't working; > >
> galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 13:47:13,951 LDAP >
> authenticate: email is unregu...@aber.ac.uk [2] >
> galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 13:47:13,951 LDAP >
> authenticate: username is None >  > galaxy.auth.providers.ldap_ad
> WARNING 2015-09-02 13:47:14,110 LDAP > authenticate: search returned
> no results > > My auth_config.xml openldap authenticator looks like
> this (edited to > remove openldap server details); > > ldap >
> '{email}'.endswith('@example.com') > > True > Challenge >
> ldaps://dc1.example.com > > ou=People,dc=dc1,dc=example,dc=com > >
> 

Re: [galaxy-dev] LDAP Auto register - "username is None"

[Martin Vickers]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi,

Okay I've solved it. The issue was that a) (mail={email}) is all that is
required in the search filter (to allow non-registered users) b) to
return cn and mail in the search-fields for use with the
auto-register-username and email. Finally, ensure auto-register is set
to True.

True
ldaps://dc1.example.com
ou=Person,dc=dc1,dc=example,dc=com
   
cn=searchuser,ou=Person,dc=dc1,dc=example,dc=com
searchpassword
cn,mail
(mail={email})
False
{dn}
{password}
{cn}
{mail}

Cheers,

Martin

On 09/03/2015 11:59 AM, Martin Vickers wrote:
> Hi Nicola,
>
> So I've realised that none of that was actually the issue. The
(&(uid={username})(mail={email})) part does work fine, it's the setting
of the username that is the issue.  When the first unregistered user
logs in, it works fine but the username is set to -10. When a second
unregistered user attempts to login, they can't. If I manually change
their username, the second user is then able to log in and once again
the username is set to -10. (see attached images).
>
> I think the issue here stems from;
>
> {uid}
>
> since I don't have a uid property in our ldap server. I've tried all
combinations of auto-register (True/False) and allow-register
(True/False/Challenge) and haven't been able to get it to work. It also
appears that auto-register-username and auto-register-email are
requirements to use this authenticator as without it noone can log in
(including registered users), and I get the following "Internal Server
Error" message.
>
> This is my current auth_config.xml file;
>
> 
> ldap
> True
> ldaps://dc1.example.com
>
ou=Person,dc=dc1,dc=example,dc=com
>
cn=searchuser,ou=Person,dc=dc1,dc=example,dc=com
> searchpasssword
> uid,mail
>
((mail={email})(uid={username}))
> False
> {dn}
> {password}
>
{uid}
> {mail}
> 
> 
>
> Doesn't one of the allow-register settings make/ask the user to
provide a username rather than trying to auto generate it? or, is there
a way to get the username out of the ldap server if it's not using uid
to store it?
>
> Many thanks,
>
> Martin
>
> On 09/02/2015 06:09 PM, Nicola Soranzo wrote:
> > Hi Martin,
> > I suspect there's an error in the sample auth_conf.xml file,
 should try to match only the email, not the username
(unless you specify True, in
which case it's viceversa) because it is not known when you first login.
In fact, for ActiveDirectory the filter is:
((objectClass=user)(mail={email}))
So, can you try to change:
((cn={username})(mail={email})) to
something like:
> > (mail={email}) Cheers, Nicola
> > On 02/09/15 15:51, Martin Vickers wrote:
> >>
>> Hi Nicola,
>>
>> It's an OpenLDAP server. uid isn't set on ours, it's cn instead, so
using ldapsearch I can correctly bind;
>>
>> dn: cn=mjv08,ou=Person,dc=dc1,dc=example,dc=com
>> objectClass: aberPerson
>> cn: mjv08
>>
>> So authentication to the ldap server is working, the issue seems to
be that when it's an unknown user, it's passing the following search string;
>>
>> (&(cn=None)(mail=unknownu...@aber.ac.uk))
>>
>> rather than;
>>
>> (&(cn=unknownuser)(mail=unknownu...@aber.ac.uk))
>>
>> hence the;
>>
>> galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 15:40:07,322 LDAP
authenticate: username is None
>> galaxy.auth.providers.ldap_ad WARNING 2015-09-02 15:40:07,485 LDAP
authenticate: search returned no results
>>
>> How is {username} in auth_config.xml set? Does it parse {email} to
get it?
>>
>> Many thanks,
>>
>> Martin
>>
>> On 09/02/2015 03:38 PM, Nicola Soranzo wrote:
>> > Hi Martin, > what LDAP server are you using? We have tested only
OpenLDAP and > ActiveDirectory, but should work on any LDAP server. > >
If it is OpenLDAP, I think you should use: > >
uid,mail >
((mail={email})(uid={username})) >
{uid} > > More details
in: > >
https://github.com/galaxyproject/galaxy/blob/dev/config/auth_conf.xml.sample
> > Cheers, > Nicola > > Il 02.09.2015 15:03 Martin Vickers ha scritto:
> > Hi All, > > I've been trying to get the new LDAP module to work. It
works fine for > existing users but I can't get auto-register to work.
In the logs I can > see the successful logins look like this; > >
galaxy.webapps.galaxy.controllers.user DEBUG 2015-09-02 13:35:06,130 >
trans.app.config.auth_config_file: ./config/auth_conf.xml >
galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 13:35:06,131 LDAP >
authenticate: email is mj...@aber.ac.uk [1] >
galaxy.auth.providers.ldap_ad DEBUG 2015-09-02 13:35:06,131 LDAP >
authenticate: username is mjv08 >  > galaxy.auth.providers.ldap_ad
DEBUG 

[galaxy-dev] PBS Torque 15007: No permission

[Ben Archuleta]

Hello All,

I have Galaxy running on the latest version of Biolinux configured to 
work with PBS/Torque version Version: 4.2.8, all jobs are being 
submitted as Debian-galaxy (This is a global user in the cluster and a 
local user on the Biolinux box).


Whenever we submit a job we get the error below:

galaxy.jobs.runners.pbs ERROR 2015-08-28 11:52:42,608 Connection to PBS 
server for submit failed: 15007: No permission


We are using: 
/usr/lib/galaxy-server/eggs/pbs_python-4.4.0-py2.7-linux-x86_64-ucs4.egg 
to interact with the PBS.



Below is how the two identical accounts are configured:

Debian-galaxy:x:2136:100::/var/lib/galaxy-server/database:/bin/fasle
Debian-galaxy:XXX:2136:100:Debian-galaxy:/var/lib/galaxy-server/database:/bin/bash


Is this a PBS Python error or could this be directly related to the PBS? 
I can submit jobs on that node by hand through Bash but not through 
Biolinux.



Thank You!
Ben
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[galaxy-dev] discover_datasets

[srodriguez]

Hi,

I am developing a tool with unknown output dataset number;
so, I am trying to use discover_datasets tag.

I have tested the following code as explained in the galaxy project
documentation:

https://bitbucket.org/galaxy/galaxy-central/raw/d1f51ff3c495b52b621ea6562ef54ba62a9205ed/test/functional/tools/multi_output_configured.xml

But, when I look at he result, I only obtain a single dataset corresponding
to the "report".
 
When I check in the job_working_directory, no "subdir(1,2 and 3)" folders
have been created and no datasets displayed on galaxy as results.

Can someone help me understand how discover_datasets work and why all the
supposed multi datasets are not displayed in the galaxy interface?

Thanks in advance.

Best regards,

Sabrina


Sabrina LEGOUEIX RODRIGUEZ
Responsable Plateau Bioinformatique
TWB - Parc technologique du canal • Bâtiment NAPA CENTER B • 3, rue  
Ariane • 31520 Ramonville Saint-Agne

Tél. : +33 (0) 5 61 28 57 92
sabrina.rodrig...@toulouse.inra.fr
www.toulouse-white-biotechnology.com
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[galaxy-dev] Error in installing tool dependencies

[Nuwan Goonasekera]

Hi,

We've encountered an error when installing tool dependencies, in
particular, with snpEff among others, on the 15.07 branch. We've tracked it
down to this particular commit and have commented on the issue there.
https://github.com/galaxyproject/galaxy/commit/91bf1d37db59bc69404e9831893bd97ae7d378f3

Should we log a trello issue?

cheers,
/Nuwan
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[galaxy-dev] Mid 2015 Galaxy CloudMan release

[Dave Clements]

*We just released an update to Galaxy CloudMan.* CloudMan offers an easy
way to get a personal and completely functional instance of Galaxy in the
cloud in just a few minutes, without any manual configuration or imposed
quotas. Once running, you have complete control over Galaxy, including the
ability to install new tools.

This is the most complete update of the Galaxy on the Cloud platform to
date with all the cloud components being built from the ground up. The
following is a summary of the major changes:

   - *Galaxy on the Cloud*: all new galaxy and indices file systems, with
   Galaxy 15.07 release, ~200 preinstalled Galaxy tools, and nearly half a
   terabyte of updated reference genome data.
   - *Galaxy on the Cloud*: switched to a different Cloud Launch
   application, available athttps://launch.usegalaxy.org/
   - *Galaxy on the Cloud*: Integrated Galaxy IPython Interactive
   Environments
   - *CloudMan*: Creating cluster shares is now fast (~30 seconds vs. hours)
   - Created a wealth of new documentation, including a description of the
   all new automated method for building private/custom instances
   https://wiki.galaxyproject.org/CloudMan/Building

See the CHANGELOG
 for a
more complete set of changes or just give it a try: see the all new Getting
Started 
 documentation.

-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/
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Re: [galaxy-dev] Installing Cairo into Gakaxy

[Christian Brenninkmeijer]

Hi,
Have you ever actually been able to run an rscript which uses the library cairo 
using this build outside of docker?
Especially on a machine that does not have a /galaxy folder?

If so did you have to install cairo into R?
Using Rscript -e "install.packages(c('Cairo_1.5-8.tar.gz')
Either directly or indirect vai a tool dependency with 

If you did install cairo into R where did you get the cairo R package from?

Christian


From: Bjoern Gruening [bjoern.gruen...@gmail.com]
Sent: Thursday, September 03, 2015 1:31 PM
To: Christian Brenninkmeijer; Björn Grüning; 
galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi Christian,

thanks for debugging. For your information we use this Docker container
to pre-build the binaries.

https://github.com/galaxyproject/docker-build/tree/master/R

So this is the place we need to fix the binaries.
Hope this helps, if I find time I will also have a look,
Bjoern

On 03.09.2015 12:10, Christian Brenninkmeijer wrote:
> In the continued effort to track down the issue of installing cairo into R
>
> I found a bug in 
> https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_1_2/41f43a2064ba
> which installs 
> https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.1.2-Linux-x84_64.tgz
>
> This has hard code paths in it.
> For example lib//pkgconfig/cairo.pc
> prefix=/galaxy/builds/Linux-x86_64/install_dir
>
> This is then picked up by cairo's configure script resulting in cairo not 
> being found as it s clearly not where galaxy said it is!
>
> Debugging continue!
>
> Christian
> University of Manchester
>
>
>
> 
> From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
> Christian Brenninkmeijer [christian.brenninkmei...@manchester.ac.uk]
> Sent: Wednesday, September 02, 2015 11:40 AM
> To: Björn Grüning; galaxy-dev@lists.galaxyproject.org; Dave Bouvier
> Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy
>
> I am still having issues installing Cairo into R
>
> I have tracked part of the problem down to:
> https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.1-Linux-x86_64.tgz
>  does have any include files so no headers.
>
> https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_2_1/3d28600fc82c has:
>   name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig
>   name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig
>
> The set_to overwrites any environment_variable PKG_CONFIG values set by other 
> packages
>
> I changed the PKG_CONFIG setting to prepend to previous values and got:
>
> checking cairo.h usability... yes
> checking cairo.h presence... yes
> checking for cairo.h... yes
> checking for PNG support in Cairo... yes
> install_environment.STDOUT DEBUG 2015-09-02 11:27:12,315 configure: 
> CAIRO_LIBS=-L/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib
>  
> -L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib
>  
> -L/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib
>  -lfreetype -lpng16 -lz -lcairo
> checking for ATS font support in Cairo... no
> configure: 
> CAIRO_LIBS=-L/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib
>  
> -L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib
>  
> -L/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib
>  -lfreetype -lpng16 -lz -lcairo
> checking for library containing deflate... none required
> install_environment.STDOUT DEBUG 2015-09-02 11:27:12,426 checking whether 
> Cairo programs can be compiled... yes
> checking whether Cairo programs can be compiled... yes
> checking whether cairo_image_surface_get_format is declared... no
> install_environment.STDOUT DEBUG 2015-09-02 11:27:12,499 checking for 
> FreeType support in cairo... yes
> install_environment.STDOUT DEBUG 2015-09-02 11:27:12,576 checking whether 
> pkg-config knows about fontconfig or freetype2... yes
> checking for FreeType support in cairo... yes
> checking whether FreeType needs additional flags... yes
> checking whether pkg-config knows about fontconfig or freetype2... yes
> checking whether additional flags work... no
> configure: error: Cannot use cairo-ft backend, although cairo claims it is 
> working. Please check your caito installation and/or update cairo if 
> necessary or set CAIRO_CFLAGS/CAIRO_LIBS accordingly.
> ERROR: configuration failed for package ‘Cairo’
>
> 
> For the record the full cmd to setup R is:
> PATH=/home/christian/galaxy/dependency_dir/pixman/0.32.4/iuc/package_pixman_0_32_4/873f53f1abcd/bin:$PATH;
>  export PATH
> 

Re: [galaxy-dev] Installing Cairo into Gakaxy

[Bjoern Gruening]

Hi Christian,

On 03.09.2015 15:14, Christian Brenninkmeijer wrote:

Hi,
Have you ever actually been able to run an rscript which uses the library cairo 
using this build outside of docker?
Especially on a machine that does not have a /galaxy folder?


Not sure about this, I simply don't know how R plots ... but we are able 
to produce a lot of different plots in a lot of different formats.





If so did you have to install cairo into R?
Using Rscript -e "install.packages(c('Cairo_1.5-8.tar.gz')
Either directly or indirect vai a tool dependency with 

If you did install cairo into R where did you get the cairo R package from?

Christian


From: Bjoern Gruening [bjoern.gruen...@gmail.com]
Sent: Thursday, September 03, 2015 1:31 PM
To: Christian Brenninkmeijer; Björn Grüning; 
galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi Christian,

thanks for debugging. For your information we use this Docker container
to pre-build the binaries.

https://github.com/galaxyproject/docker-build/tree/master/R

So this is the place we need to fix the binaries.
Hope this helps, if I find time I will also have a look,
Bjoern

On 03.09.2015 12:10, Christian Brenninkmeijer wrote:

In the continued effort to track down the issue of installing cairo into R

I found a bug in 
https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_1_2/41f43a2064ba
which installs 
https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.1.2-Linux-x84_64.tgz

This has hard code paths in it.
For example lib//pkgconfig/cairo.pc
prefix=/galaxy/builds/Linux-x86_64/install_dir

This is then picked up by cairo's configure script resulting in cairo not being 
found as it s clearly not where galaxy said it is!

Debugging continue!

Christian
University of Manchester




From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Christian Brenninkmeijer [christian.brenninkmei...@manchester.ac.uk]
Sent: Wednesday, September 02, 2015 11:40 AM
To: Björn Grüning; galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

I am still having issues installing Cairo into R

I have tracked part of the problem down to:
https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.1-Linux-x86_64.tgz 
does have any include files so no headers.

https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_2_1/3d28600fc82c has:
  $INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig
  $INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig

The set_to overwrites any environment_variable PKG_CONFIG values set by other 
packages

I changed the PKG_CONFIG setting to prepend to previous values and got:

checking cairo.h usability... yes
checking cairo.h presence... yes
checking for cairo.h... yes
checking for PNG support in Cairo... yes
install_environment.STDOUT DEBUG 2015-09-02 11:27:12,315 configure: 
CAIRO_LIBS=-L/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib
 
-L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib
 
-L/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib
 -lfreetype -lpng16 -lz -lcairo
checking for ATS font support in Cairo... no
configure: 
CAIRO_LIBS=-L/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib
 
-L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib
 
-L/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib
 -lfreetype -lpng16 -lz -lcairo
checking for library containing deflate... none required
install_environment.STDOUT DEBUG 2015-09-02 11:27:12,426 checking whether Cairo 
programs can be compiled... yes
checking whether Cairo programs can be compiled... yes
checking whether cairo_image_surface_get_format is declared... no
install_environment.STDOUT DEBUG 2015-09-02 11:27:12,499 checking for FreeType 
support in cairo... yes
install_environment.STDOUT DEBUG 2015-09-02 11:27:12,576 checking whether 
pkg-config knows about fontconfig or freetype2... yes
checking for FreeType support in cairo... yes
checking whether FreeType needs additional flags... yes
checking whether pkg-config knows about fontconfig or freetype2... yes
checking whether additional flags work... no
configure: error: Cannot use cairo-ft backend, although cairo claims it is 
working. Please check your caito installation and/or update cairo if necessary 
or set CAIRO_CFLAGS/CAIRO_LIBS accordingly.
ERROR: configuration failed for package ‘Cairo’


For the record the full cmd to setup R is:
PATH=/home/christian/galaxy/dependency_dir/pixman/0.32.4/iuc/package_pixman_0_32_4/873f53f1abcd/bin:$PATH;
 export PATH

Re: [galaxy-dev] Installing Cairo into Gakaxy

[Christian Brenninkmeijer]

Thanks Bjoern,

At this point I am looking to run a tiny R script which just loads Cairo and 
reports the session Info.

Full Rscript which would be run via r_wrapper.sh
===
library(Cairo)

args<-commandArgs(TRUE)
writeLines(capture.output(sessionInfo()), args[1])
sessionInfo()


Even that fails so at the moment saying Cairo library can not be found.
This is because SCDE we want to use depends on Cairo

Christian

From: Bjoern Gruening [bjoern.gruen...@gmail.com]
Sent: Thursday, September 03, 2015 2:20 PM
To: Christian Brenninkmeijer; Bjoern Gruening; 
galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi Christian,

On 03.09.2015 15:14, Christian Brenninkmeijer wrote:
> Hi,
> Have you ever actually been able to run an rscript which uses the library 
> cairo using this build outside of docker?
> Especially on a machine that does not have a /galaxy folder?

Not sure about this, I simply don't know how R plots ... but we are able
to produce a lot of different plots in a lot of different formats.



> If so did you have to install cairo into R?
> Using Rscript -e "install.packages(c('Cairo_1.5-8.tar.gz')
> Either directly or indirect vai a tool dependency with  type="setup_r_environment">
>
> If you did install cairo into R where did you get the cairo R package from?
>
> Christian
>
> 
> From: Bjoern Gruening [bjoern.gruen...@gmail.com]
> Sent: Thursday, September 03, 2015 1:31 PM
> To: Christian Brenninkmeijer; Björn Grüning; 
> galaxy-dev@lists.galaxyproject.org; Dave Bouvier
> Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy
>
> Hi Christian,
>
> thanks for debugging. For your information we use this Docker container
> to pre-build the binaries.
>
> https://github.com/galaxyproject/docker-build/tree/master/R
>
> So this is the place we need to fix the binaries.
> Hope this helps, if I find time I will also have a look,
> Bjoern
>
> On 03.09.2015 12:10, Christian Brenninkmeijer wrote:
>> In the continued effort to track down the issue of installing cairo into R
>>
>> I found a bug in 
>> https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_1_2/41f43a2064ba
>> which installs 
>> https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.1.2-Linux-x84_64.tgz
>>
>> This has hard code paths in it.
>> For example lib//pkgconfig/cairo.pc
>> prefix=/galaxy/builds/Linux-x86_64/install_dir
>>
>> This is then picked up by cairo's configure script resulting in cairo not 
>> being found as it s clearly not where galaxy said it is!
>>
>> Debugging continue!
>>
>> Christian
>> University of Manchester
>>
>>
>>
>> 
>> From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
>> Christian Brenninkmeijer [christian.brenninkmei...@manchester.ac.uk]
>> Sent: Wednesday, September 02, 2015 11:40 AM
>> To: Björn Grüning; galaxy-dev@lists.galaxyproject.org; Dave Bouvier
>> Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy
>>
>> I am still having issues installing Cairo into R
>>
>> I have tracked part of the problem down to:
>> https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.1-Linux-x86_64.tgz
>>  does have any include files so no headers.
>>
>> https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_2_1/3d28600fc82c has:
>>   > name="PKG_CONFIG_DIR">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig
>>   > name="PKG_CONFIG_PATH">$INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig
>>
>> The set_to overwrites any environment_variable PKG_CONFIG values set by 
>> other packages
>>
>> I changed the PKG_CONFIG setting to prepend to previous values and got:
>>
>> checking cairo.h usability... yes
>> checking cairo.h presence... yes
>> checking for cairo.h... yes
>> checking for PNG support in Cairo... yes
>> install_environment.STDOUT DEBUG 2015-09-02 11:27:12,315 configure: 
>> CAIRO_LIBS=-L/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib
>>  
>> -L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib
>>  
>> -L/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib
>>  -lfreetype -lpng16 -lz -lcairo
>> checking for ATS font support in Cairo... no
>> configure: 
>> CAIRO_LIBS=-L/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib
>>  
>> -L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib
>>  
>> -L/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib
>>  -lfreetype -lpng16 -lz -lcairo
>> checking for library containing deflate... none required
>> install_environment.STDOUT DEBUG 2015-09-02 11:27:12,426 checking whether 
>> Cairo programs can be compiled... yes
>> checking whether Cairo programs can be compiled... 

Re: [galaxy-dev] Installing Cairo into Gakaxy

[Bjoern Gruening]

Hi Christian,

thanks for debugging. For your information we use this Docker container 
to pre-build the binaries.


https://github.com/galaxyproject/docker-build/tree/master/R

So this is the place we need to fix the binaries.
Hope this helps, if I find time I will also have a look,
Bjoern

On 03.09.2015 12:10, Christian Brenninkmeijer wrote:

In the continued effort to track down the issue of installing cairo into R

I found a bug in 
https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_1_2/41f43a2064ba
which installs 
https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.1.2-Linux-x84_64.tgz

This has hard code paths in it.
For example lib//pkgconfig/cairo.pc
prefix=/galaxy/builds/Linux-x86_64/install_dir

This is then picked up by cairo's configure script resulting in cairo not being 
found as it s clearly not where galaxy said it is!

Debugging continue!

Christian
University of Manchester




From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
Christian Brenninkmeijer [christian.brenninkmei...@manchester.ac.uk]
Sent: Wednesday, September 02, 2015 11:40 AM
To: Björn Grüning; galaxy-dev@lists.galaxyproject.org; Dave Bouvier
Subject: Re: [galaxy-dev] Installing Cairo into Gakaxy

I am still having issues installing Cairo into R

I have tracked part of the problem down to:
https://depot.galaxyproject.org/package/linux/x86_64/R/R-3.2.1-Linux-x86_64.tgz 
does have any include files so no headers.

https://testtoolshed.g2.bx.psu.edu/view/iuc/package_r_3_2_1/3d28600fc82c has:
 $INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig
 $INSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig

The set_to overwrites any environment_variable PKG_CONFIG values set by other 
packages

I changed the PKG_CONFIG setting to prepend to previous values and got:

checking cairo.h usability... yes
checking cairo.h presence... yes
checking for cairo.h... yes
checking for PNG support in Cairo... yes
install_environment.STDOUT DEBUG 2015-09-02 11:27:12,315 configure: 
CAIRO_LIBS=-L/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib
 
-L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib
 
-L/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib
 -lfreetype -lpng16 -lz -lcairo
checking for ATS font support in Cairo... no
configure: 
CAIRO_LIBS=-L/home/christian/galaxy/dependency_dir/cairo/1.12.14/iuc/package_cairo_1_12_14/5c25a57405a9/lib
 
-L/home/christian/galaxy/dependency_dir/freetype/2.5.2/iuc/package_freetype_2_5_2/8999860ddf69/lib
 
-L/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib
 -lfreetype -lpng16 -lz -lcairo
checking for library containing deflate... none required
install_environment.STDOUT DEBUG 2015-09-02 11:27:12,426 checking whether Cairo 
programs can be compiled... yes
checking whether Cairo programs can be compiled... yes
checking whether cairo_image_surface_get_format is declared... no
install_environment.STDOUT DEBUG 2015-09-02 11:27:12,499 checking for FreeType 
support in cairo... yes
install_environment.STDOUT DEBUG 2015-09-02 11:27:12,576 checking whether 
pkg-config knows about fontconfig or freetype2... yes
checking for FreeType support in cairo... yes
checking whether FreeType needs additional flags... yes
checking whether pkg-config knows about fontconfig or freetype2... yes
checking whether additional flags work... no
configure: error: Cannot use cairo-ft backend, although cairo claims it is 
working. Please check your caito installation and/or update cairo if necessary 
or set CAIRO_CFLAGS/CAIRO_LIBS accordingly.
ERROR: configuration failed for package ‘Cairo’


For the record the full cmd to setup R is:
PATH=/home/christian/galaxy/dependency_dir/pixman/0.32.4/iuc/package_pixman_0_32_4/873f53f1abcd/bin:$PATH;
 export PATH
PIXMAN_LIB_PATH=/home/christian/galaxy/dependency_dir/pixman/0.32.4/iuc/package_pixman_0_32_4/873f53f1abcd/lib;
 export PIXMAN_LIB_PATH
PKG_CONFIG_PATH=/home/christian/galaxy/dependency_dir/pixman/0.32.4/iuc/package_pixman_0_32_4/873f53f1abcd/lib/pkgconfig:$PKG_CONFIG_PATH;
 export PKG_CONFIG_PATH
PATH=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/bin:$PATH;
 export PATH
LIBPNG_ROOT=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6;
 export LIBPNG_ROOT
LIBPNG_LIB_PATH=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib;
 export LIBPNG_LIB_PATH
LIBPNG_INCLUDE_PATH=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/include;
 export LIBPNG_INCLUDE_PATH
LD_LIBRARY_PATH=/home/christian/galaxy/dependency_dir/libpng/1.6.7/iuc/package_libpng_1_6_7/ac6ef08bf0e6/lib:$LD_LIBRARY_PATH;
 export LD_LIBRARY_PATH