Advice on Galaxy administration
Dear all, I'm still new to Galaxy but was wondering if someone could offer some advice. On a local Galaxy instance, if I were the Galaxy administrator but do not have sudo access on the machine itself, is this a problem? Or are the two roles intricately linked so that the Galaxy administrator will have to pester the system administrator frequently? The web interface alone is not sufficient for the Galaxy administrator. (i.e., does a Galaxy administrator need sudo access ... or even just group access to the Galaxy subdirectory to effectively do his/her job? ...I mean making Galaxy owned by a Unix group and putting the Galaxy administrator in that group.) As an aside, I was trying to do some alignment with bwa and realized I needed to prepare the genome by creating the index and an accompanying .loc file. The instructions [1] seem to imply some kind of command-line access.. Thank you for your help! Ray [1] https://wiki.galaxyproject.org/Admin/DataPreparation
Hi Ray, You will absolutely need command line access to the Galaxy server for some of the administration tasks - the web admin controls and web report tool only let you do some of the likely tasks. During the initial setup admin (sudo) rights would be useful, at very least you'll need the sys admin to help with mounting shared network drives, cluster integration, database setup. If you want to run cluster jobs as the associated Unix account of each user, or anything like LDAP logins, then again you will need help from your sys admin. See also: https://wiki.galaxyproject.org/Community/GalaxyAdmins Peter On Tue, Sep 22, 2015 at 9:07 AM, Raymond Wan <rwan.work@gmail.com> wrote:
Dear all,
I'm still new to Galaxy but was wondering if someone could offer some advice.
On a local Galaxy instance, if I were the Galaxy administrator but do not have sudo access on the machine itself, is this a problem? Or are the two roles intricately linked so that the Galaxy administrator will have to pester the system administrator frequently? The web interface alone is not sufficient for the Galaxy administrator.
(i.e., does a Galaxy administrator need sudo access ... or even just group access to the Galaxy subdirectory to effectively do his/her job? ...I mean making Galaxy owned by a Unix group and putting the Galaxy administrator in that group.)
As an aside, I was trying to do some alignment with bwa and realized I needed to prepare the genome by creating the index and an accompanying .loc file. The instructions [1] seem to imply some kind of command-line access..
Thank you for your help!
Ray
[1] https://wiki.galaxyproject.org/Admin/DataPreparation ___________________________________________________________ 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: https://lists.galaxyproject.org/
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Hello everyone, I'm trying to set up a Galaxy instance on a multi-core server in my university so according to the instructions here: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS I installed Torque, changed the eggs.ini file by adding the 4.4.0. version of pbs_python and tried to setup pbs_python via scramble: LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python When I did that I got the error: Failed to find log.h in inlcude dir /usr/include/torque. (Set incude dir via PBS_PYTHON_INCLUDEDIR variable) Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 57, in scramble self.run_scramble_script() File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 210, in run_scramble_script raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) ) galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for pbs_python 4.4.0 so I did some digging around and found that the file I need is in /scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/ (please correct me if I am wrong) So I tried again using: PBS_PYTHON_INCLUDEDIR=/home/galaxy/galaxy/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/ LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python but then I got the error: In file included from src/C++/pbs_ifl.h:90:0, from src/C++/pbs_wrap.cxx:2978: /usr/local/include/u_hash_map_structs.h:82:25: fatal error: container.hpp: No such file or directory #include "container.hpp" Can someone help me please? Kind regards, Makis
Here is an old thread that looks rather similar to your problems: https://www.mail-archive.com/galaxy-dev@lists.galaxyproject.org/msg00078.htm... -Will On Tue, Sep 22, 2015 at 2:43 AM, Makis Ladoukakis <makis4ever@hotmail.com> wrote:
Hello everyone,
I'm trying to set up a Galaxy instance on a multi-core server in my university so according to the instructions here:
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS
I installed Torque, changed the eggs.ini file by adding the 4.4.0. version of pbs_python
and tried to setup pbs_python via scramble:
LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python
When I did that I got the error:
Failed to find log.h in inlcude dir /usr/include/torque. (Set incude dir via PBS_PYTHON_INCLUDEDIR variable) Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 57, in scramble self.run_scramble_script() File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 210, in run_scramble_script raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) ) galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for pbs_python 4.4.0
so I did some digging around and found that the file I need is in
/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/
(please correct me if I am wrong)
So I tried again using:
PBS_PYTHON_INCLUDEDIR=/home/galaxy/galaxy/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/ LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python
but then I got the error:
In file included from src/C++/pbs_ifl.h:90:0, from src/C++/pbs_wrap.cxx:2978: /usr/local/include/u_hash_map_structs.h:82:25: fatal error: container.hpp: No such file or directory #include "container.hpp"
Can someone help me please?
Kind regards, Makis
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email.
Hello Will, Thank you for your reply. I had already checked this thread before as I browsed through the mailing list for "pbs_python" issues. It doesn't have the same errors (can't locate log.h and when i provide it it wants the container.hpp ) and up to one point i've already followed the "rescrambling" of the pbs_python. Anyone else had any experience with that? Thank you, Makis Date: Tue, 22 Sep 2015 09:35:11 -0700 Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble From: wholtz@lygos.com To: makis4ever@hotmail.com CC: galaxy-dev@lists.galaxyproject.org Here is an old thread that looks rather similar to your problems:https://www.mail-archive.com/galaxy-dev@lists.galaxyproject.org/msg00078.htm... -Will On Tue, Sep 22, 2015 at 2:43 AM, Makis Ladoukakis <makis4ever@hotmail.com> wrote: Hello everyone, I'm trying to set up a Galaxy instance on a multi-core server in my university so according to the instructions here: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS I installed Torque, changed the eggs.ini file by adding the 4.4.0. version of pbs_python and tried to setup pbs_python via scramble: LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python When I did that I got the error: Failed to find log.h in inlcude dir /usr/include/torque. (Set incude dir via PBS_PYTHON_INCLUDEDIR variable) Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 57, in scramble self.run_scramble_script() File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 210, in run_scramble_script raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) ) galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for pbs_python 4.4.0 so I did some digging around and found that the file I need is in /scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/ (please correct me if I am wrong) So I tried again using: PBS_PYTHON_INCLUDEDIR=/home/galaxy/galaxy/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/ LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python but then I got the error: In file included from src/C++/pbs_ifl.h:90:0, from src/C++/pbs_wrap.cxx:2978: /usr/local/include/u_hash_map_structs.h:82:25: fatal error: container.hpp: No such file or directory #include "container.hpp" Can someone help me please? Kind regards, Makis ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email.
Hi Makis, The thread I posted does have the exact same container.hpp error and proposes a solution. Did you try setting your PBS_PYTHON_INCLUDEDIR to point to your torque/include directory, as mentioned in that thread? from the thread: export PBS_PYTHON_INCLUDEDIR=/usr/local/torque/include/ export PBSCONFIG=/usr/local/torque/bin/pbs-config export LIBTORQUE_DIR=/usr/local/torque/lib/libtorque.so -Will On Wed, Sep 23, 2015 at 5:49 AM, Makis Ladoukakis <makis4ever@hotmail.com> wrote:
Hello Will,
Thank you for your reply. I had already checked this thread before as I browsed through the mailing list for "pbs_python" issues. It doesn't have the same errors (can't locate log.h and when i provide it it wants the container.hpp ) and up to one point i've already followed the "rescrambling" of the pbs_python.
Anyone else had any experience with that?
Thank you, Makis
------------------------------ Date: Tue, 22 Sep 2015 09:35:11 -0700 Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble From: wholtz@lygos.com To: makis4ever@hotmail.com CC: galaxy-dev@lists.galaxyproject.org
Here is an old thread that looks rather similar to your problems:
https://www.mail-archive.com/galaxy-dev@lists.galaxyproject.org/msg00078.htm...
-Will
On Tue, Sep 22, 2015 at 2:43 AM, Makis Ladoukakis <makis4ever@hotmail.com> wrote:
Hello everyone,
I'm trying to set up a Galaxy instance on a multi-core server in my university so according to the instructions here:
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS
I installed Torque, changed the eggs.ini file by adding the 4.4.0. version of pbs_python
and tried to setup pbs_python via scramble:
LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python
When I did that I got the error:
Failed to find log.h in inlcude dir /usr/include/torque. (Set incude dir via PBS_PYTHON_INCLUDEDIR variable) Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 57, in scramble self.run_scramble_script() File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 210, in run_scramble_script raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) ) galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for pbs_python 4.4.0
so I did some digging around and found that the file I need is in
/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/
(please correct me if I am wrong)
So I tried again using:
PBS_PYTHON_INCLUDEDIR=/home/galaxy/galaxy/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/ LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python
but then I got the error:
In file included from src/C++/pbs_ifl.h:90:0, from src/C++/pbs_wrap.cxx:2978: /usr/local/include/u_hash_map_structs.h:82:25: fatal error: container.hpp: No such file or directory #include "container.hpp"
Can someone help me please?
Kind regards, Makis
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers).
Please consider the environment before printing this email.
-- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email.
Hello Will, Thanks again for your reply. Yes I had already tried these but I got the same container.hpp error. The only thing different in my case is that the names of the directories of the directories are a bit different: export PBS_PYTHON_INCLUDEDIR=/usr/local/include/ export PBSCONFIG=/usr/local/bin/pbs-config export LIBTORQUE_DIR=/usr/local/lib/libtorque.so python scripts/scramble.py -e pbs_python Any ideas? Kind regards, Makis Date: Wed, 23 Sep 2015 07:06:32 -0700 Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble From: wholtz@lygos.com To: makis4ever@hotmail.com CC: galaxy-dev@lists.galaxyproject.org Hi Makis, The thread I posted does have the exact same container.hpp error and proposes a solution. Did you try setting your PBS_PYTHON_INCLUDEDIR to point to your torque/include directory, as mentioned in that thread? from the thread:export PBS_PYTHON_INCLUDEDIR=/usr/local/torque/include/ export PBSCONFIG=/usr/local/torque/bin/pbs-config export LIBTORQUE_DIR=/usr/local/torque/lib/libtorque.so -Will On Wed, Sep 23, 2015 at 5:49 AM, Makis Ladoukakis <makis4ever@hotmail.com> wrote: Hello Will, Thank you for your reply. I had already checked this thread before as I browsed through the mailing list for "pbs_python" issues. It doesn't have the same errors (can't locate log.h and when i provide it it wants the container.hpp ) and up to one point i've already followed the "rescrambling" of the pbs_python. Anyone else had any experience with that? Thank you, Makis Date: Tue, 22 Sep 2015 09:35:11 -0700 Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble From: wholtz@lygos.com To: makis4ever@hotmail.com CC: galaxy-dev@lists.galaxyproject.org Here is an old thread that looks rather similar to your problems:https://www.mail-archive.com/galaxy-dev@lists.galaxyproject.org/msg00078.htm... -Will On Tue, Sep 22, 2015 at 2:43 AM, Makis Ladoukakis <makis4ever@hotmail.com> wrote: Hello everyone, I'm trying to set up a Galaxy instance on a multi-core server in my university so according to the instructions here: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS I installed Torque, changed the eggs.ini file by adding the 4.4.0. version of pbs_python and tried to setup pbs_python via scramble: LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python When I did that I got the error: Failed to find log.h in inlcude dir /usr/include/torque. (Set incude dir via PBS_PYTHON_INCLUDEDIR variable) Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 57, in scramble self.run_scramble_script() File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 210, in run_scramble_script raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) ) galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for pbs_python 4.4.0 so I did some digging around and found that the file I need is in /scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/ (please correct me if I am wrong) So I tried again using: PBS_PYTHON_INCLUDEDIR=/home/galaxy/galaxy/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/ LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python but then I got the error: In file included from src/C++/pbs_ifl.h:90:0, from src/C++/pbs_wrap.cxx:2978: /usr/local/include/u_hash_map_structs.h:82:25: fatal error: container.hpp: No such file or directory #include "container.hpp" Can someone help me please? Kind regards, Makis ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email. -- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email.
And does find /usr/local/include -name container.hpp or find / -name container.hpp return torque/src/include/container.hpp ? My guess is you installed binaries for Torque, but the scrambling requires the Torque source (or at least the header files form Torque). -Will On Thu, Sep 24, 2015 at 1:16 AM, Makis Ladoukakis <makis4ever@hotmail.com> wrote:
Hello Will,
Thanks again for your reply. Yes I had already tried these but I got the same container.hpp error.
The only thing different in my case is that the names of the directories of the directories are a bit different:
export PBS_PYTHON_INCLUDEDIR=/usr/local/include/ export PBSCONFIG=/usr/local/bin/pbs-config export LIBTORQUE_DIR=/usr/local/lib/libtorque.so python scripts/scramble.py -e pbs_python
Any ideas?
Kind regards, Makis
------------------------------ Date: Wed, 23 Sep 2015 07:06:32 -0700
Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble From: wholtz@lygos.com To: makis4ever@hotmail.com CC: galaxy-dev@lists.galaxyproject.org
Hi Makis,
The thread I posted does have the exact same container.hpp error and proposes a solution.
Did you try setting your PBS_PYTHON_INCLUDEDIR to point to your torque/include directory, as mentioned in that thread?
from the thread:
export PBS_PYTHON_INCLUDEDIR=/usr/local/torque/include/ export PBSCONFIG=/usr/local/torque/bin/pbs-config export LIBTORQUE_DIR=/usr/local/torque/lib/libtorque.so
-Will
On Wed, Sep 23, 2015 at 5:49 AM, Makis Ladoukakis <makis4ever@hotmail.com> wrote:
Hello Will,
Thank you for your reply. I had already checked this thread before as I browsed through the mailing list for "pbs_python" issues. It doesn't have the same errors (can't locate log.h and when i provide it it wants the container.hpp ) and up to one point i've already followed the "rescrambling" of the pbs_python.
Anyone else had any experience with that?
Thank you, Makis
------------------------------ Date: Tue, 22 Sep 2015 09:35:11 -0700 Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble From: wholtz@lygos.com To: makis4ever@hotmail.com CC: galaxy-dev@lists.galaxyproject.org
Here is an old thread that looks rather similar to your problems:
https://www.mail-archive.com/galaxy-dev@lists.galaxyproject.org/msg00078.htm...
-Will
On Tue, Sep 22, 2015 at 2:43 AM, Makis Ladoukakis <makis4ever@hotmail.com> wrote:
Hello everyone,
I'm trying to set up a Galaxy instance on a multi-core server in my university so according to the instructions here:
https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS
I installed Torque, changed the eggs.ini file by adding the 4.4.0. version of pbs_python
and tried to setup pbs_python via scramble:
LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python
When I did that I got the error:
Failed to find log.h in inlcude dir /usr/include/torque. (Set incude dir via PBS_PYTHON_INCLUDEDIR variable) Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 57, in scramble self.run_scramble_script() File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 210, in run_scramble_script raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) ) galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for pbs_python 4.4.0
so I did some digging around and found that the file I need is in
/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/
(please correct me if I am wrong)
So I tried again using:
PBS_PYTHON_INCLUDEDIR=/home/galaxy/galaxy/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/ LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python
but then I got the error:
In file included from src/C++/pbs_ifl.h:90:0, from src/C++/pbs_wrap.cxx:2978: /usr/local/include/u_hash_map_structs.h:82:25: fatal error: container.hpp: No such file or directory #include "container.hpp"
Can someone help me please?
Kind regards, Makis
___________________________________________________________ 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: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers).
Please consider the environment before printing this email.
-- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers).
Please consider the environment before printing this email.
-- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email.
Hi Peter, On Tue, Sep 22, 2015 at 5:18 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Ray,
You will absolutely need command line access to the Galaxy server for some of the administration tasks - the web admin controls and web report tool only let you do some of the likely tasks.
During the initial setup admin (sudo) rights would be useful, at very least you'll need the sys admin to help with mounting shared network drives, cluster integration, database setup. If you want to run cluster jobs as the associated Unix account of each user, or anything like LDAP logins, then again you will need help from your sys admin.
I see! Sorry to go off on a tangent, but something I'm marginally familiar with is content management systems (CMS) such as Joomla and WordPress and maybe I can use it as an analogy to make sure I understand. For those, suppose we create an account "ray" who owns or is in a group with the Apache process who owns: 1) the directory that Joomla resides in and all subdirectories, 2) is the database administrator of the MySQL database, and 3) is the administrator of the Joomla web interface then I wouldn't need sudo access. On occasion, the Apache configuration might need to be changed and the system administrator can be asked to do that, but that's probably once a year or something. Is Galaxy like this? Or do you reckon I need full sudo access? Sorry, I just want to make sure when I ask for greater access, I have an idea how Galaxy works or how it might differ from a CMS.
See also: https://wiki.galaxyproject.org/Community/GalaxyAdmins
Thanks for the link! I'll take a look at it to get myself better acquainted with administering Galaxy! Ray
On Tue, Sep 22, 2015 at 4:38 PM, Raymond Wan <rwan.work@gmail.com> wrote:
Hi Peter,
On Tue, Sep 22, 2015 at 5:18 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Ray,
You will absolutely need command line access to the Galaxy server for some of the administration tasks - the web admin controls and web report tool only let you do some of the likely tasks.
During the initial setup admin (sudo) rights would be useful, at very least you'll need the sys admin to help with mounting shared network drives, cluster integration, database setup. If you want to run cluster jobs as the associated Unix account of each user, or anything like LDAP logins, then again you will need help from your sys admin.
I see!
Sorry to go off on a tangent, but something I'm marginally familiar with is content management systems (CMS) such as Joomla and WordPress and maybe I can use it as an analogy to make sure I understand. For those, suppose we create an account "ray" who owns or is in a group with the Apache process who owns:
1) the directory that Joomla resides in and all subdirectories, 2) is the database administrator of the MySQL database, and 3) is the administrator of the Joomla web interface
then I wouldn't need sudo access. On occasion, the Apache configuration might need to be changed and the system administrator can be asked to do that, but that's probably once a year or something.
Is Galaxy like this? Or do you reckon I need full sudo access?
Sorry, I just want to make sure when I ask for greater access, I have an idea how Galaxy works or how it might differ from a CMS.
There are certainly similarities with the CMS idea - Galaxy also has its own user accounts, and interacts with Apache. I would certainly opt for a galaxy Linux user account with minimal rights (no sudo!), which would own all the files by default, and also galaxy specific database accounts (probably PostgreSQL not MySQL). We then install various Galaxy specific dependencies like samtools under $HOME/bin which is on the Galaxy user's $PATH - which like the main Tool Shed dependency mechanism installs tools locally without needing sys admin rights on the Galaxy server or cluster. When I have needed sudo has been during Galaxy setup (often), but only occasionally since (e.g. debugging and needing to restart services, or changing Apache settings). Peter
Hi Peter, Thank you for the prompt reply and the clear answer! Indeed, I don't want to ask for more than what I need (i.e., sudo) since that would scare a lot of people. However, I'd like to strike a balance and be able to help users without pestering the system administrators too much. With administrator rights to just the Galaxy interface, I felt like my hands were tied in terms of resolving some of the issues I was seeing with the bwa toolbox. It seems I was right. I will see what could be done in terms of gaining command-line access to the Galaxy directory. Thank you for your advice! Ray On Wed, Sep 23, 2015 at 12:12 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Tue, Sep 22, 2015 at 4:38 PM, Raymond Wan <rwan.work@gmail.com> wrote:
Hi Peter,
On Tue, Sep 22, 2015 at 5:18 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Ray,
You will absolutely need command line access to the Galaxy server for some of the administration tasks - the web admin controls and web report tool only let you do some of the likely tasks.
During the initial setup admin (sudo) rights would be useful, at very least you'll need the sys admin to help with mounting shared network drives, cluster integration, database setup. If you want to run cluster jobs as the associated Unix account of each user, or anything like LDAP logins, then again you will need help from your sys admin.
I see!
Sorry to go off on a tangent, but something I'm marginally familiar with is content management systems (CMS) such as Joomla and WordPress and maybe I can use it as an analogy to make sure I understand. For those, suppose we create an account "ray" who owns or is in a group with the Apache process who owns:
1) the directory that Joomla resides in and all subdirectories, 2) is the database administrator of the MySQL database, and 3) is the administrator of the Joomla web interface
then I wouldn't need sudo access. On occasion, the Apache configuration might need to be changed and the system administrator can be asked to do that, but that's probably once a year or something.
Is Galaxy like this? Or do you reckon I need full sudo access?
Sorry, I just want to make sure when I ask for greater access, I have an idea how Galaxy works or how it might differ from a CMS.
There are certainly similarities with the CMS idea - Galaxy also has its own user accounts, and interacts with Apache.
I would certainly opt for a galaxy Linux user account with minimal rights (no sudo!), which would own all the files by default, and also galaxy specific database accounts (probably PostgreSQL not MySQL).
We then install various Galaxy specific dependencies like samtools under $HOME/bin which is on the Galaxy user's $PATH - which like the main Tool Shed dependency mechanism installs tools locally without needing sys admin rights on the Galaxy server or cluster.
When I have needed sudo has been during Galaxy setup (often), but only occasionally since (e.g. debugging and needing to restart services, or changing Apache settings).
Peter
participants (4)
-
Makis Ladoukakis -
Peter Cock -
Raymond Wan -
Will Holtz