Re: [galaxy-dev] pbs_python can't be installed via scramble
Here is an old thread that looks rather similar to your problems: https://www.mail-archive.com/galaxy-dev@lists.galaxyproject.org/msg00078.html -Will On Tue, Sep 22, 2015 at 2:43 AM, Makis Ladoukakis 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 > 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 who...@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. ___ 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/
Re: [galaxy-dev] Advice on Galaxy administration
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 wrote: > On Tue, Sep 22, 2015 at 4:38 PM, Raymond Wan wrote: >> Hi Peter, >> >> >> On Tue, Sep 22, 2015 at 5:18 PM, Peter Cock >> 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 ___ 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/
Re: [galaxy-dev] Advice on Galaxy administration
On Tue, Sep 22, 2015 at 4:38 PM, Raymond Wan wrote: > Hi Peter, > > > On Tue, Sep 22, 2015 at 5:18 PM, Peter Cock 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 ___ 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/
[galaxy-dev] Current directory in the galaxy job file script
I installed the latest Galaxy (v15.07) and tested with a job. I found my local environment setup file was not executed. The line of code that executes the local setup file is [ -f "config/local_env.sh" ] && . config/local_env.sh Further looking into the galaxy_xx.sh file shows the current directory of the script is $working_directory before "cd $working_directory" is executed. This is not the case in previous versions, where the job's current directory is the root of the Galaxy server in the beginning, until "cd $working_directory" is executed. I think making the current directory first at the root of the Galaxy server is better since I don't need to put a full path in galaxy.ini for the environment_setup_file. Will you change this back to it was? Thanks, Ping ___ 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/
Re: [galaxy-dev] Galaxy on a Cluster -- Active Directory LDAP configuration
Hi Carlos, We aren’t using Active Directory here – but we do use an OpenLDAP directory which our cluster authenticates against, as does Galaxy. In order to track cluster usage for users running Galaxy jobs we use galaxy-pulsar between Galaxy itself and our SLURM cluster. Pulsar is configured to submit all jobs as a real user on the cluster, via SLURM-DRMAA. This means that all of the Galaxy usage on the cluster appears in our SLURM accounting database just like any other job would. The complexity here is file ownership. Pulsar has to copy all input files into a staging directory, and change ownership to the real user for the job to run on the cluster. It is/was(?) a little complex to setup, as there are more parts involved then a typical Galaxy install, but it works great for us here. When I was getting this setup John Chilton mentioned adding a PulsarEmbedded runner into Galaxy at some point. Not sure whether this has/is happening, but it’d make these situations easier: https://trello.com/c/4YwVZBtq/1865-embedded-pulsar-job-runner DT -- David Trudgian Ph.D. Computational Scientist, BioHPC UT Southwestern Medical Center Dallas, TX 75390-9039 Tel: (214) 648-4833 From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On Behalf Of Nicola Soranzo Sent: Tuesday, September 22, 2015 5:59 AM To: Carlos Lijeron ; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev] Galaxy on a Cluster -- Active Directory LDAP configuration Hi Carlos, we are using Active Directory LDAP for user authentication, which works pretty well, but only the Galaxy user to submit jobs to the LSF cluster queue, so I can't help with the resource tracking. Cheers, Nicola On 21/09/15 20:19, Carlos Lijeron wrote: Everyone, We are setting up Galaxy to work with our cluster and SLURM as the work manager. The cluster itself authenticates to our local Active Directory, so I’m wondering if the best way to track resource utilization of Galaxy users on the cluster is to also have Galaxy authenticate to the same Active Directory LDAP. Is anyone on this list using the same configuration and tracking resource utilization from Galaxy users submitting jobs to the cluster nodes? Please advise. Thank you all ! Carlos. ___ 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/ UT Southwestern Medical Center The future of medicine, today. ___ 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/
Re: [galaxy-dev] Advice on Galaxy administration
Hi Peter, On Tue, Sep 22, 2015 at 5:18 PM, Peter Cock 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 ___ 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/
[galaxy-dev] uWSGI --daemonize option should be replaced with --daemonize2
Hello guys, I'm configuring a new Galaxy production instance and I did many tries with uWSGI. I have found that the -d (or --daemonize) option that the Galaxy wiki suggests should be replaced with the --daemonize2 option. In fact, when using the -d option for uWSGI it often happens that some (or sometimes all) of the uwsgi workers does not correctly bind to the Galaxy app when uWSGI is loaded just after Galaxy, as when you set up an init.d galaxy launch script. I don't know exactly why it happens but I think it has to do with the fact that uWSGI daemonize before the Galaxy server is fully loaded and this was giving me a lot of headaches. Example: This is a typical uWSGI log that I had at launch when using -d (or --daemonize) using six workers spawned uWSGI master process (pid: 32142) spawned uWSGI worker 1 (pid: 32183, cores: 4) spawned uWSGI worker 2 (pid: 32184, cores: 4) spawned uWSGI worker 3 (pid: 32185, cores: 4) galaxy.queue_worker INFO 2015-09-22 13:53:22,348 Binding and starting galaxy control worker for main.1 galaxy.queue_worker INFO 2015-09-22 13:53:22,351 Binding and starting galaxy control worker for main.2 spawned uWSGI worker 4 (pid: 32188, cores: 4) spawned uWSGI worker 5 (pid: 32189, cores: 4) galaxy.queue_worker INFO 2015-09-22 13:53:22,356 Binding and starting galaxy control worker for main.4 spawned uWSGI worker 6 (pid: 32191, cores: 4) *** Stats server enabled on 127.0.0.1:9191 fd: 20 *** galaxy.queue_worker INFO 2015-09-22 13:53:22,360 Binding and starting galaxy control worker for main.5 As you can see worker 3 and worker 6 are not bound to galaxy. And this behaviour is not deterministic: sometimes more workers are missing and in some cases I had no workers bound to Galaxy and so it was not accessible. Some other times instead all the workers were correctly bound to Galaxy. Using --daemonize2 ensures that uWSGI daemonize after the app (Galaxy) is fully loaded thus removing this strange behaviour. Best, Federico ___ 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/
Re: [galaxy-dev] parse history file/uploaded file with dynamic_options script
Hi Greg, Wow that was easy! I was not expecting that. Thank you! Linda On 09/22/2015 03:41 PM, Von Kuster, Greg wrote: Hi Linda, I think your parameter definition will need to send the file_name of the HistoryDatasetAssociation, something like this... In my dynamic_options.py script, I want to parse the headers from 'amplitudes' file and show them in the checkboxes section. My problem seems to be the following. In python, amplitudes is a galaxy object: How do I parse/access this file to get the headers? It seems to be partly the same problem as asked last week in this conversation: http://dev.list.galaxyproject.org/Question-about-using-dynamic-options-and-refresh-on-change-for-rendering-2-associated-select-lists-td4667943.html Thanks! Linda -- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bak...@wur.nl ___ 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/ -- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bak...@wur.nl ___ 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/
Re: [galaxy-dev] parse history file/uploaded file with dynamic_options script
Hi Linda, I think your parameter definition will need to send the file_name of the HistoryDatasetAssociation, something like this... > > > > > In my dynamic_options.py script, I want to parse the headers from > 'amplitudes' file and show them in the checkboxes section. > > My problem seems to be the following. > > In python, amplitudes is a galaxy object: > > > How do I parse/access this file to get the headers? > > It seems to be partly the same problem as asked last week in this > conversation: > http://dev.list.galaxyproject.org/Question-about-using-dynamic-options-and-refresh-on-change-for-rendering-2-associated-select-lists-td4667943.html > > > Thanks! > Linda > > -- > Linda Bakker > Bioinformatics Research Assistant > Plant Research International, Wageningen UR > Building 107 (Radix), room W1.Fa.054 > Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands > tel: +31-317-480756 > email: linda.bak...@wur.nl > > ___ > 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/ ___ 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/
[galaxy-dev] Time Out
Hello, i'm repeatexplorer user and i am with difficult for download of a archive. The archive weighs 13.5GB and always arriving at 600-700MB of download, the download fail. I need a solution. Thank you. -- Daniel Siqueira de Oliveira Acadêmico de Ciências Biológicas- UFSM Iniciação científica- LABDROS Fone: (55)- 9699-5834 ___ 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/
[galaxy-dev] parse history file/uploaded file with dynamic_options script
Hi All, I am a bit lost here. In my xml I have the following sections: label="amplitude file"/> display="checkboxes" multiple="true" label="Mark quality control samples" dynamic_options='get_column_names(amplitudes)'/> In my dynamic_options.py script, I want to parse the headers from 'amplitudes' file and show them in the checkboxes section. My problem seems to be the following. In python, amplitudes is a galaxy object: How do I parse/access this file to get the headers? It seems to be partly the same problem as asked last week in this conversation: http://dev.list.galaxyproject.org/Question-about-using-dynamic-options-and-refresh-on-change-for-rendering-2-associated-select-lists-td4667943.html Thanks! Linda -- Linda Bakker Bioinformatics Research Assistant Plant Research International, Wageningen UR Building 107 (Radix), room W1.Fa.054 Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands tel: +31-317-480756 email: linda.bak...@wur.nl ___ 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/
Re: [galaxy-dev] Galaxy on a Cluster -- Active Directory LDAP configuration
Hi Carlos, we are using Active Directory LDAP for user authentication, which works pretty well, but only the Galaxy user to submit jobs to the LSF cluster queue, so I can't help with the resource tracking. Cheers, Nicola On 21/09/15 20:19, Carlos Lijeron wrote: Everyone, We are setting up Galaxy to work with our cluster and SLURM as the work manager. The cluster itself authenticates to our local Active Directory, so I’m wondering if the best way to track resource utilization of Galaxy users on the cluster is to also have Galaxy authenticate to the same Active Directory LDAP. Is anyone on this list using the same configuration and tracking resource utilization from Galaxy users submitting jobs to the cluster nodes? Please advise. Thank you all ! Carlos. ___ 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/ ___ 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/
[galaxy-dev] pbs_python can't be installed via scramble
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 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/
Re: [galaxy-dev] Advice on Galaxy administration
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 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] 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 ___ 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/