Re: [galaxy-dev] Mail is not configured for this Galaxy instance.
Hi Hans-Rudolf, Apologies for the delay.Thank you very nuch for your help.My problem solved successfully after 'smtp_server' settings in my universe_wsgi.ini file. shenwiyn From: Hans-Rudolf Hotz Date: 2013-07-31 23:40 To: shenwiyn CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Mail is not configured for this Galaxy instance. Hi Shenwiyn You need to specify a SMTP server. Have a look at the 'smtp_server' settings in your universe_wsgi.ini file. Regards, Hans-Rudolf On 07/31/2013 04:19 PM, shenwiyn wrote: Hi everyone, In my local Galaxy,when I want to reset my Login password,some error occurre :Mail is not configured for this Galaxy instance. Please contact an administrator. Could anyone tell me some imformation about how to configure the mail for my Galaxy instance? Thank you very much. shenwiyn ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Select in Filter and Sort fail to work.
Galaxy Tearm, I use Select in Filter and Sort to sort my sam file in my local Galaxy.But I got no peek under Matching pattern: ^@ ,while I got the same sam file under NOT Matching pattern: ^@ .Actually,I can got the correct results in Galaxy main,I don't know what happened to my local Galaxy .I use 009088d5e76f as my local Galaxy. my sam file as follow: @HD VN:1.0 SO:coordinate @RG ID:rg1 SM:s1 @RG ID:rg2 SM:s3 @SQ SN:chr1 LN:10001 @SQ SN:chr2 LN:11 @SQ SN:chr3 LN:10001 @SQ SN:chr4 LN:1001 bar:record:1 141 chr1 20 0 * * 0 0 C 2 RG:Z:rg1 bar:record:1 77 chr1 10 0 * * 0 0 A 1 RG:Z:rg1 bar:record:2 141 chr2 30 0 * * 0 0 C 2 RG:Z:rg2 bar:record:2 77 chr2 10 0 * * 0 0 A 1 RG:Z:rg1 bar:record:3 141 chr3 20 0 * * 0 0 C 2 RG:Z:rg1 bar:record:3 77 chr1 10 0 * * 0 0 A 1 RG:Z:rg2 bar:record:4 141 chr1 40 0 * * 0 0 C 2 RG:Z:rg1 bar:record:4 77 chr1 1 0 * * 0 0 A 1 RG:Z:rg1 bar:record:5 141 chr3 40 0 * * 0 0 C 2 RG:Z:rg1 bar:record:5 77 chr1 40 0 * * 0 0 A 1 RG:Z:rg2 bar:record:6 141 chr1 50 0 * * 0 0 C 2 RG:Z:rg2 bar:record:6 77 chr1 1 0 * * 0 0 A 1 RG:Z:rg2 bar:record:7 141 chr4 20 0 * * 0 0 C 2 RG:Z:rg1 bar:record:7 77 chr1 20 0 * * 0 0 A 1 RG:Z:rg2 bar:record:8 141 chr3 20 0 * * 0 0 C 2 RG:Z:rg1 bar:record:8 77 chr1 30 0 * * 0 0 A 1 RG:Z:rg2 bar:record:9 141 chr4 60 0 * * 0 0 C 2 RG:Z:rg1 bar:record:9 77 chr4 10 0 * * 0 0 A 1 RG:Z:rg1 shenwiy___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Can not find hg_g1k_v37.fa.
Hi everyone, I want to use the hg_g1k_v37.fa on my local Galaxy,but I can not find this data.When I use the command : rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/hg_g1k_v37/seq/hg_g1k_v37.fa the error occurred: receiving incremental file list rsync: link_stat /hg_g1k_v37/seq/hg_g1k_v37.fa (in indexes) failed: No such file or directory (2) sent 4 bytes received 6 bytes 4.00 bytes/sec total size is 0 speedup is 0.00 rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1532) [receiver=3.0.6] Please any suggestions would be most welcome. Thanks. shenwiyn___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] How to configure and set up the Circos on my local Galaxy?
Hi , I found that the visualization of Circos works greatly in Galaxy main,but failed on my local Galaxy.I want to find out some information about configuring and setting up the Circos on local Galaxy,I saw nothing in http://wiki.galaxyproject.org/New%20Visualization%20Page#Circos_plot_.28aka_Circster.29 .Please any suggestions would be most welcome. shenwiyn___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Help with cluster setup
Yes,and I also have the same confuse about that.Actually when I set server:id in the universe_wsgi.ini as follows for a try,my Galaxy doesn't work with Cluster,if I remove server:id,it work . [server:node01] use = egg:Paste#http port = 8080 host = 0.0.0.0 use_threadpool = true threadpool_workers = 5 This is my job_conf.xml : ?xml version=1.0? job_conf plugins workers=4 plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner workers=4/ plugin id=pbs type=runner load=galaxy.jobs.runners.pbs:PBSJobRunner workers=8/ /plugins handlers default=batch handler id=node01 tags=batch/ handler id=node02 tags=batch/ /handlers destinations default=regularjobs destination id=local runner=local/ destination id=regularjobs runner=pbs tags=cluster param id=Resource_Listwalltime=24:00:00,nodes=1:ppn=4,mem=10G/param param id=galaxy_external_runjob_scriptscripts/drmaa_external_runner.py/param param id=galaxy_external_killjob_scriptscripts/drmaa_external_killer.py/param param id=galaxy_external_chown_scriptscripts/external_chown_script.py/param /destination /destinations /job_conf Further more when I want to kill my jobs by clicking in galaxy web,the job keeps on running in my background.I do not know how to fix this. Any help on this would be grateful.Thank you very much. shenwiyn From: Jurgens de Bruin Date: 2013-08-07 19:55 To: galaxy-dev Subject: [galaxy-dev] Help with cluster setup Hi, This is my first Galaxy installation setup so apologies for stupid questions. I am setting up Galaxy on a Cluster running Torque as the resource manager. I am working through the documentation but I am unclear on some things: Firstly I am unable to find : start_job_runners within the universe_wsgi.ini and I dont want to just add this anywhere - any help on this would be create. Further more this is my job_conf.xml : ?xml version=1.0? !-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -- job_conf plugins plugin id=hpc type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner workers=4/ /plugins handlers !-- Additional job handlers - the id should match the name of a [server:id] in universe_wsgi.ini. handler id=cn01/ handler id=cn02/ /handlers destinations destination id=hpc runner=drmaa/ /destinations /job_conf Does this look meaning full, further more where to I set the additional server:id in the universe_wsgi.ini. As background the cluster has 13 compute nodes and a shared storage array that can be accessed by all nodes in the cluster. Thanks again -- Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/ distinti saluti/siong/duì yú/привет Jurgens de Bruin Catch(08-08-09-12-39).jpg___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Mail is not configured for this Galaxy instance.
Hi Hans-Rudolf, Thank you very much for you help.Actually I want some more information about how to configure 'smtp_server' in universe_wsgi.ini.Could you show me some samples to have a look please? Regards, shenwiyn From: Hans-Rudolf Hotz Date: 2013-07-31 23:40 To: shenwiyn CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Mail is not configured for this Galaxy instance. Hi Shenwiyn You need to specify a SMTP server. Have a look at the 'smtp_server' settings in your universe_wsgi.ini file. Regards, Hans-Rudolf On 07/31/2013 04:19 PM, shenwiyn wrote: Hi everyone, In my local Galaxy,when I want to reset my Login password,some error occurre :Mail is not configured for this Galaxy instance. Please contact an administrator. Could anyone tell me some imformation about how to configure the mail for my Galaxy instance? Thank you very much. shenwiyn ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Galaxy jobs running on cluster can't stop.
Hi everyone, I run my galaxy jobs of Megablast on cluster ,but when I want to kill my Megablast by clicking , the job keeps on running in my background.The job_conf.xml I set as follows: destination id=long_jobs runner=pbs tags=cluster param id=Resource_Listwalltime=72:00:00,nodes=2:ppn=8,mem=16G/param param id=galaxy_external_runjob_scriptscripts/drmaa_external_runner.py/param param id=galaxy_external_killjob_scriptscripts/drmaa_external_killer.py/param param id=galaxy_external_chown_scriptscripts/external_chown_script.py/param /destination tools tool id=megablast_wrapper destination=long_jobs/ /tools Could anyone give me some help please?Thank you. shenwiynCatch.jpg___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] reference genomes missing
Hi, I think you can get reference genomes from UCSC,and then make Bowtie2 index data by bowtie2-build.Other way you can try rsync to get the index files ,for more information you can see http://wiki.galaxyproject.org/Admin/Data%20Integration . Hope to help you. shenwiyn From: Gerald Bothe Date: 2013-08-01 01:16 To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] reference genomes missing I installed a local instance of GALAXY following the instructions at Get Galaxy ... in the Wiki. It installed ok, but when I tried the Bowtie2 mapper with a test data set, I noticed that the reference genomes are missing. How can I get the reference genomes (e.g. latest version of mouse and human) and integrate them into Galaxy? Or is there a Galaxy version available that has the genomes already installed? Thanks Gerald ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Build the Galaxy under Cluster
Hi Carlos, Thank you very much for your help.I use Galaxy with the torque2.5.0,pbs_python for a test.It seems to work successfully ! shenwiyn From: Carlos Borroto Date: 2013-07-10 01:49 To: shenwiyn CC: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Build the Galaxy under Cluster Hi shenwyn, This is a very generic question hard to answer. I can tell you I use Galaxy with the torque 4.1.x branch, maui scheduler and pbs-drmaa. I would suggest you take a look a this[1] wiki page. Please notice as it is mentioned in that page, using libdrmaa.so from torque won't work, I can confirm that. [1]http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster Hope it helps, Carlos On Tue, Jul 2, 2013 at 5:50 AM, shenwiyn shenw...@gmail.com wrote: Hi everyone, I want to install my local Galaxy under the Cluster with TORQUE.I have a question about how they work together successfully.In addition,after my local Galaxy and TORQUE install successfully,anything else should I do to the Cluster Galaxy?Thank you very much. shenwiyn ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] shall us specify which tool run in cluster?
Hi Thon Deboer , I am a newer in Galaxy.I installed my Galaxy with Torque2.5.0 ,and Galaxy uses the pbs_modoule to interface with TORQUE.But I have some question of the job_conf.xml : 1.)In your job_conf.xml ,you use regularjobs,longjobs,shortjobs...to run different jobs ,how our Galaxy know which tool belongs to regularjobs or longjobs.And what is the meaning of nativeSpecification? 2.)Shall us use toolscollection of tool id=bwa_wrapper destination=multicorejobs4/to specify bwa ?Does it mean the bwa belong to multicorejobs4,and run in cluster? 3.)Does every tool need us to specify which job it belong to? I saw http://wiki.galaxyproject.org/Admin/Config/Jobs about this,but I am not sure above.Could you help me please? shenwiyn From: Thon Deboer Date: 2013-07-18 14:31 To: galaxy-dev Subject: [galaxy-dev] Jobs remain in queue until restart Hi, I have noticed that from time to time, the job queue seems to be “stuck” and can only be unstuck by restarting galaxy. The jobs seem to be in the queue state and the python job handler processes are hardly ticking over and the cluster is empty. When I restart, the startup procedure realizes all jobs are in the a “new state” and it then assigns a jobhandler after which the jobs start fine…. Any ideas? Torque Thon P.S I am using the june version of galaxy and I DO set limits on my users in job_conf.xml as so: (Maybe it is related? Before it went into dormant mode, this user had started lots of jobs and may have hit the limit, but I assumed this limit was the number of running jobs at one time, right?) ?xml version=1.0? job_conf plugins workers=4 !-- workers is the number of threads for the runner's work queue. The default from plugins is used if not defined for a plugin. -- plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner workers=2/ plugin id=drmaa type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner workers=8/ plugin id=cli type=runner load=galaxy.jobs.runners.cli:ShellJobRunner workers=2/ /plugins handlers default=handlers !-- Additional job handlers - the id should match the name of a [server:id] in universe_wsgi.ini. -- handler id=handler0 tags=handlers/ handler id=handler1 tags=handlers/ handler id=handler2 tags=handlers/ handler id=handler3 tags=handlers/ !-- handler id=handler10 tags=handlers/ handler id=handler11 tags=handlers/ handler id=handler12 tags=handlers/ handler id=handler13 tags=handlers/ -- /handlers destinations default=regularjobs !-- Destinations define details about remote resources and how jobs should be executed on those remote resources. -- destination id=local runner=local/ destination id=regularjobs runner=drmaa tags=cluster !-- These are the parameters for qsub, such as queue etc. -- param id=nativeSpecification-V -q long.q -pe smp 1/param /destination destination id=longjobs runner=drmaa tags=cluster,long_jobs !-- These are the parameters for qsub, such as queue etc. -- param id=nativeSpecification-V -q long.q -pe smp 1/param /destination destination id=shortjobs runner=drmaa tags=cluster,short_jobs !-- These are the parameters for qsub, such as queue etc. -- param id=nativeSpecification-V -q short.q -pe smp 1/param /destination destination id=multicorejobs4 runner=drmaa tags=cluster,multicore_jobs !-- These are the parameters for qsub, such as queue etc. -- param id=nativeSpecification-V -q long.q -pe smp 4/param /destination !-- destination id=real_user_cluster runner=drmaa param id=galaxy_external_runjob_scriptscripts/drmaa_external_runner.py/param param id=galaxy_external_killjob_scriptscripts/drmaa_external_killer.py/param param id=galaxy_external_chown_scriptscripts/external_chown_script.py/param /destination -- destination id=dynamic runner=dynamic !-- A destination that represents a method in the dynamic runner. -- param id=typepython/param param id=functioninteractiveOrCluster/param /destination /destinations tools !-- Tools can be configured to use specific destinations or handlers, identified by either the id or tags attribute. If assigned to a tag, a handler or destination that matches that tag will be chosen at random. -- tool id=bwa_wrapper destination=multicorejobs4/ /tools limits !-- Certain limits can be defined. limit type=registered_user_concurrent_jobs500/limit limit type=unregistered_user_concurrent_jobs1/limit limit type=concurrent_jobs id=local1/limit
[galaxy-dev] Mail is not configured for this Galaxy instance.
Hi everyone, In my local Galaxy,when I want to reset my Login password,some error occurre :Mail is not configured for this Galaxy instance. Please contact an administrator. Could anyone tell me some imformation about how to configure the mail for my Galaxy instance? Thank you very much. shenwiyn___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] job_conf.xml questions
Hi Ido Tamir, I have the same question too. I set megablast as long_jobs for the test,when I cancel my megablast job in Galaxy history before it finishs,it still work in my background.The drmaa_external_killer.py seems doesn't work.I don't know where is the problem,and hope someone can help me . a) In my advanced example I have: destination id=long_jobs runner=pbs tags=cluster param id=Resource_Listwalltime=72:00:00,nodes=2:ppn=8,mem=16G/param param id=galaxy_external_runjob_scriptscripts/drmaa_external_runner.py/param param id=galaxy_external_killjob_scriptscripts/drmaa_external_killer.py/param param id=galaxy_external_chown_scriptscripts/external_chown_script.py/param /destination tools tool id=ucsc_tablebrowser destination=regularjobs/ tool id=megablast_wrapper destination=long_jobs/ /tools b)In my background,I get the qstat result : Job idName UserTime Use S Queue - --- - - 46.server ...n...@genomics.cn galaxy 00:00:00 R batch shenwiyn From: Ido Tamir Date: 2013-07-23 21:53 To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] job_conf.xml questions Hi, I work myself through the job_conf.xml and have a question: a) In your advanced example you have: destination id=remote_cluster runner=drmaa tags=longjobs/ destination id=real_user_cluster runner=drmaa !-- TODO: The real user options should maybe not be considered runner params. -- param id=galaxy_external_runjob_scriptscripts/drmaa_external_runner.py/param param id=galaxy_external_killjob_scriptscripts/drmaa_external_killer.py/param param id=galaxy_external_chown_scriptscripts/external_chown_script.py/param /destination Does this mean that remote_cluster jobs can not be killed unless I add the 3 scripts to this destination? Or does this have to do with the run jobs as real user that I don't need currently. I am using the galaxy user for all jobs for the moment? To phrase this differently: Do I need these three scripts? b) Can I set a wall time limit for only for my local runners? like: destination id=local runner=local/ param id=Resource_Listwalltime=72:00:00/param /destination When I set it in limits, will it work for local runners and then I have to override it in every destination? thank you very much, ido ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] job_conf.xml about running Galaxy tools on a cluster.
Hi everyone， I am a newer in Galaxy. I installed my Galaxy with Torque2.5.0 . I used my job_conf.xml for a test ,my Galaxy seems to work with TORQUE by the interface of pbs_modoule ( _pbs.so) successfully. In my test job_conf.xml , it seems that we should use toolscollection of tool id=bwa_wrapper destination=multicorejobs4/to specify bwa to run as multicorejobs4. But I do not sure wheather all the tools in Galaxy we should specify their destination (such as, regularjobs,longjobs), or all the tools would work with a default destination(destinations default=regularjobs).,unless we specify them. Could anyone give me some help please? This is my test job_conf.xml: ?xml version=1.0? job_conf plugins workers=4 !-- workers is the number of threads for the runner's work queue. The default from plugins is used if not defined for a plugin.-- plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner workers=2/ plugin id=pbs type=runner load=galaxy.jobs.runners.pbs:PBSJobRunner workers=8/ /plugins handlers default=batch !-- Additional job handlers - the id should match the name of a [server:id] in universe_wsgi.ini. -- handler id=node01 tags=batch/ handler id=node02 tags=batch/ !-- handler id=handler10 tags=handlers/ handler id=handler11 tags=handlers/ handler id=handler12 tags=handlers/ handler id=handler13 tags=handlers/ -- /handlers destinations default=regularjobs !-- Destinations define details about remote resources and how jobs should be executed on those remote resources. -- destination id=local runner=local/ destination id=regularjobs runner=pbs tags=cluster !-- These are the parameters for qsub, such as queue etc. -- /destination destination id=longjobs runner=pbs tags=cluster,long_jobs !-- These are the parameters for qsub, such as queue etc. -- /destination destination id=shortjobs runner=pbs tags=cluster,short_jobs !-- These are the parameters for qsub, such as queue etc. -- /destination destination id=multicorejobs runner=pbs tags=cluster,multicore_jobs !-- These are the parameters for qsub, such as queue etc. -- /destination destination id=real_user_cluster runner=pbs param id=galaxy_external_runjob_scriptscripts/drmaa_external_runner.py/param param id=galaxy_external_killjob_scriptscripts/drmaa_external_killer.py/param param id=galaxy_external_chown_scriptscripts/external_chown_script.py/param /destination destination id=dynamic runner=dynamic !-- A destination that represents a method in the dynamic runner. -- param id=typepython/param param id=functioninteractiveOrCluster/param /destination /destinations tools !-- Tools can be configured to use specific destinations or handlers, identified by either the id or tags attribute. If assigned to a tag, a handler or destination that matches that tag will be chosen at random.-- tool id=bwa_wrapper destination=multicorejobs/ /tools limits !-- Certain limits can be defined.-- limit type=registered_user_concurrent_jobs500/limit limit type=unregistered_user_concurrent_jobs1/limit limit type=concurrent_jobs id=local1/limit limit type=concurrent_jobs tag=cluster200/limit limit type=concurrent_jobs tag=long_jobs200/limit limit type=concurrent_jobs tag=short_jobs200/limit limit type=concurrent_jobs tag=multicore_jobs100/limit /limits /job_conf shenwiyn___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] shall us specify which tool run in cluster?
Hi Thon Deboer , I am a newer in Galaxy.I installed my Galaxy with Torque2.5.0 ,and Galaxy uses the pbs_modoule to interface with TORQUE.But I have some question of the job_conf.xml : 1.)In your job_conf.xml ,you use regularjobs,longjobs,shortjobs...to run different jobs ,how our Galaxy know which tool belongs to regularjobs or longjobs.And what is the meaning of nativeSpecification? 2.)Shall us use toolscollection of tool id=bwa_wrapper destination=multicorejobs4/to specify bwa ?Does it mean the bwa belong to multicorejobs4,and run in cluster? 3.)Does every tool need us to specify which job it belong to? I saw http://wiki.galaxyproject.org/Admin/Config/Jobs about this,but I am not sure above.Could you help me please? shenwiyn From: Thon Deboer Date: 2013-07-18 14:31 To: galaxy-dev Subject: [galaxy-dev] Jobs remain in queue until restart Hi, I have noticed that from time to time, the job queue seems to be “stuck” and can only be unstuck by restarting galaxy. The jobs seem to be in the queue state and the python job handler processes are hardly ticking over and the cluster is empty. When I restart, the startup procedure realizes all jobs are in the a “new state” and it then assigns a jobhandler after which the jobs start fine…. Any ideas? Torque Thon P.S I am using the june version of galaxy and I DO set limits on my users in job_conf.xml as so: (Maybe it is related? Before it went into dormant mode, this user had started lots of jobs and may have hit the limit, but I assumed this limit was the number of running jobs at one time, right?) ?xml version=1.0? job_conf plugins workers=4 !-- workers is the number of threads for the runner's work queue. The default from plugins is used if not defined for a plugin. -- plugin id=local type=runner load=galaxy.jobs.runners.local:LocalJobRunner workers=2/ plugin id=drmaa type=runner load=galaxy.jobs.runners.drmaa:DRMAAJobRunner workers=8/ plugin id=cli type=runner load=galaxy.jobs.runners.cli:ShellJobRunner workers=2/ /plugins handlers default=handlers !-- Additional job handlers - the id should match the name of a [server:id] in universe_wsgi.ini. -- handler id=handler0 tags=handlers/ handler id=handler1 tags=handlers/ handler id=handler2 tags=handlers/ handler id=handler3 tags=handlers/ !-- handler id=handler10 tags=handlers/ handler id=handler11 tags=handlers/ handler id=handler12 tags=handlers/ handler id=handler13 tags=handlers/ -- /handlers destinations default=regularjobs !-- Destinations define details about remote resources and how jobs should be executed on those remote resources. -- destination id=local runner=local/ destination id=regularjobs runner=drmaa tags=cluster !-- These are the parameters for qsub, such as queue etc. -- param id=nativeSpecification-V -q long.q -pe smp 1/param /destination destination id=longjobs runner=drmaa tags=cluster,long_jobs !-- These are the parameters for qsub, such as queue etc. -- param id=nativeSpecification-V -q long.q -pe smp 1/param /destination destination id=shortjobs runner=drmaa tags=cluster,short_jobs !-- These are the parameters for qsub, such as queue etc. -- param id=nativeSpecification-V -q short.q -pe smp 1/param /destination destination id=multicorejobs4 runner=drmaa tags=cluster,multicore_jobs !-- These are the parameters for qsub, such as queue etc. -- param id=nativeSpecification-V -q long.q -pe smp 4/param /destination !-- destination id=real_user_cluster runner=drmaa param id=galaxy_external_runjob_scriptscripts/drmaa_external_runner.py/param param id=galaxy_external_killjob_scriptscripts/drmaa_external_killer.py/param param id=galaxy_external_chown_scriptscripts/external_chown_script.py/param /destination -- destination id=dynamic runner=dynamic !-- A destination that represents a method in the dynamic runner. -- param id=typepython/param param id=functioninteractiveOrCluster/param /destination /destinations tools !-- Tools can be configured to use specific destinations or handlers, identified by either the id or tags attribute. If assigned to a tag, a handler or destination that matches that tag will be chosen at random. -- tool id=bwa_wrapper destination=multicorejobs4/ /tools limits !-- Certain limits can be defined. limit type=registered_user_concurrent_jobs500/limit limit type=unregistered_user_concurrent_jobs1/limit limit type=concurrent_jobs id=local1/limit
Re: [galaxy-dev] Build the Galaxy under Cluster
Hi Carlos, Thank you very much for your help.I use Galaxy with the torque2.5.0,pbs_python for a test.It seems to work successfully ! shenwiyn From: Carlos Borroto Date: 2013-07-10 01:49 To: shenwiyn CC: galaxy-...@bx.psu.edu Subject: Re: [galaxy-dev] Build the Galaxy under Cluster Hi shenwyn, This is a very generic question hard to answer. I can tell you I use Galaxy with the torque 4.1.x branch, maui scheduler and pbs-drmaa. I would suggest you take a look a this[1] wiki page. Please notice as it is mentioned in that page, using libdrmaa.so from torque won't work, I can confirm that. [1]http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster Hope it helps, Carlos On Tue, Jul 2, 2013 at 5:50 AM, shenwiyn shenw...@gmail.com wrote: Hi everyone, I want to install my local Galaxy under the Cluster with TORQUE.I have a question about how they work together successfully.In addition,after my local Galaxy and TORQUE install successfully,anything else should I do to the Cluster Galaxy?Thank you very much. shenwiyn ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Build the Galaxy under Cluster
Hi everyone, I want to install my local Galaxy under the Cluster with TORQUE.I have a question about how they work together successfully.In addition,after my local Galaxy and TORQUE install successfully,anything else should I do to the Cluster Galaxy?Thank you very much. shenwiyn___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Build the Galaxy under Cluster
Hi everyone, I want to install my local Galaxy under the Cluster with TORQUE.I have a question about how they work together successfully.In addition,after my local Galaxy and TORQUE install successfully,anything else should I do to the Cluster Galaxy?Thank you very much. shenwiyn___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] where the log in information saved?
Hi everyone, I installed my local galaxy successfully.But I have a problem about how to find out the log in information of each user ,such as the register mail and the password .And which files do this informations saved? Thank you! shenwiyn___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Error of GATK tools test
Hi everyone, I have installed GATK tools in my local galaxy .But when I want to test whether they work successfully ,something error appear: The error appears under the BAM files we input : Unspecified genome build, click the pencil icon in the history item to set the genome build Could anyone tell me how to test the GATK tools and why this error appear?Thank you very much for you help. shenwiyn___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] indexes file of Megablast
Hi everyone, I have some questions about the tool of Megablast in NGS:Mapping when I download the needed indexes . There are four indexes files we need for Megablast:htgs 28-Jan-2013 ,nt 28-Jan-2013,wgs 28-Jan-2013,phiX174;but there are too many types of the indexes file in ftp://ftp.ncbi.nlm.nih.gov/blast/db/ ,for example : nt.00.tar.gz,nt.01.tar.gz,nt.02.tar.gzI don't know the difference among these files ,and I don't which one I should choose to download.In addition ,I can't find the index file for phiX174. Could anyone help me and give me some advice please? Thank you very much. shenwiyn___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Problem running Tophat for Illumina
Hi everyone, I also have this confusion between bowtie/bowtie2 and tophat/tophat2 on our local galaxy.Have all of these we need to installed? Actually,Map with Bowtie for Illumina and Map with Bowtie for SOLiD depend on the bowtie-0.12.8 ,Bowtie2 just depends on bowtie2-2.0.2.If we just install bowtie-0.12.8 ,we should get rid of Bowtie2,and the same as tophat/tophat2,and if we keep all of the functions ,all of these we need to installed,right? shenwiyn From: greg Date: 2013-02-22 01:22 To: Jennifer Jackson CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Problem running Tophat for Illumina Ok, you're right, I did ask something similar before. So is the simplest answer is to tell users to use Tophat2 instead of Tophat for Illumina? Or is there anything special in Tophat for Illumina that they would be missing out on? -Greg Here's some info I dug up in case it's useful: which bowtie /usr/local/galaxy/installs/bin/bowtie-0.12.8/bowtie which tophat /usr/local/galaxy/installs/bin/tophat-2.0.6.Linux_x86_64/tophat I do have all of these installed: bowtie-0.12.8 bowtie2-2.0.2 bwa-0.6.2 cufflinks-2.0.2.Linux_x86_64 tophat-2.0.6.Linux_x86_64 Here's the PATH if it helps: echo $PATH /misc/local/galaxy/galaxy_python/bin:/sge/8.0.1p4/bin/lx-amd64:/usr/lib64/qt-3.3/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/pinerog/bin:/usr/local.orig/bin:/usr/local/R-2.15.0/bin/:/usr/local/blast+:/usr/local/EMBOSS:/usr/local/galaxy/installs/bin/beam2:/usr/local/galaxy/installs/bin/bowtie2-2.0.2:/usr/local/galaxy/installs/bin/bowtie2-2.0.2/scripts:/usr/local/galaxy/installs/bin/bowtie-0.12.8:/usr/local/galaxy/installs/bin/bowtie-0.12.8/scripts:/usr/local/galaxy/installs/bin/tophat-2.0.6.Linux_x86_64:/usr/local/galaxy/installs/bin/samtools-0.1.18:/usr/local/galaxy/installs/bin/samtools-0.1.18/misc:/usr/local/galaxy/installs/bin/samtools-0.1.18/bcftools:/usr/local/galaxy/installs/bin/cufflinks-2.0.2.Linux_x86_64:/usr/local/galaxy/installs/bin/express-1.2.2-linux_x86_64:/usr/local/galaxy/installs/bin/bwa-0.6.2:/usr/local/galaxy/installs/bin/fastx:/usr/local/galaxy/installs/bin/lastz-distrib-1.02.00:/usr/local/ga! laxy/installs/bin/lastz-distrib-1.02.00/tools:/misc/local/galaxy/galaxy_python/bin On Thu, Feb 21, 2013 at 11:40 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Greg, The problem here and the confusion between the Bowtie loc files are likely related. Do you have both bowtie/bowtie2 and tophat/tophat2 installed? And the tool wrappers for all versions are active? I though we resolved this earlier but maybe you installed a new tool or updated? The wrappers for the tools that have dependencies on bowtie vs bowtie2 (and the associated indexes) are not interchangeable. You will need to chech your paths to see which tool is being used for each - be sure to check any symbolic paths that may have been created when the tools were installed (these tools are known to create links such as bowtie - bowtie2, that you will want to get rid of). Reviewing tool dependencies is the best way to troubleshoot: http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies Hopefully this helps. Be sure to keep any followup on the mailing list so the dev community can continue to have input, Jen Galaxy team On 2/21/13 7:50 AM, greg wrote: Hi guys, On our local galaxy install I'm getting the error below when I run tophat for illumina like this: http://snag.gy/HsWyS.jpg Any ideas? Thanks, Greg Error: Dataset generation errors Dataset 27: Tophat for Illumina on data 15: deletions Tool execution generated the following error message: Error in tophat: tophat: option --no-closure-search not recognized for detailed help see http://tophat.cbcb.umd.edu/manual.html cp: cannot stat `/home/galaxy/job_working_directory/000/238/tophat_out/junctions.bed': No such file or directory cp: cannot stat `/home/galaxy/job_working_directory/000/238/tophat_out/insertions.bed': No such file or directory cp: cannot stat `/home/galaxy/job_working_directory/000/238/tophat_out/accepted_hits.bam': No such file or directory cp: cannot stat `/home/galaxy/job_working_directory/000/238/tophat_out/deletions.bed': No such file or directory The tool produced the following additional output: TopHat v2.0.6 tophat -p 4 -a 8 -m 0 -i 70 -I 50 -g 20 --library-type fr-unstranded --max-insertion-length 3 --max-deletion-length 3 --coverage-search --min-coverage-intron 50 --max-coverage-intron 2 --no-closure-search --initial-read-mismatches 2 --segment-mismatches 2 --segment-length 25 --min-segment-intron 50 --max-segment-intron 50 /usr/local/galaxy/indexes/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome /home/galaxy/000/dataset_306.dat ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions
Re: [galaxy-dev] Tools and Data
Hi Enis Afgan, Thank you very much for you answer. I have some questions abount the tool of Megablast in NGS:Mapping when I download the needed indexes . There are four indexes files we need for Megablast:htgs 28-Jan-2013 ,nt 28-Jan-2013,wgs 28-Jan-2013,phiX174;but there are too many types of the indexes file in ftp://ftp.ncbi.nlm.nih.gov/blast/db/ ,for example : nt.00.tar.gz,nt.01.tar.gz,nt.02.tar.gzI don't know the differents among these files ,and I don't which one I should choose to download.In addition ,I can't find the index file for phiX174. Could you help me and give me some advice please? Thanks. shenwiyn From: Enis Afgan Date: 2013-03-05 10:38 To: shenwiyn CC: Rafael Hernández; galaxy-...@bx.psu.edu Subject: Re: Tools and Data Correct; certain NSG tools require additional configuration for their indices (http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup) On Tue, Mar 5, 2013 at 1:07 PM, shenwiyn shenw...@gmail.com wrote: Hi, I've installed Galaxy in local as what Rafael does.I want to make sure that the basic functions work successfully just depending on the necessary tools in Tool dependencies manual,and the NGS tools not only depend on the necessary tools but also some another needed data(such as indexes,and so on). thakks shenwy___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Tools and Data
Hi, I have some questions about the tool of Megablast in NGS:Mapping when I download the needed indexes . There are four indexes files we need for Megablast:htgs 28-Jan-2013 ,nt 28-Jan-2013,wgs 28-Jan-2013,phiX174;but there are too many types of the indexes file in ftp://ftp.ncbi.nlm.nih.gov/blast/db/ ,for example : nt.00.tar.gz,nt.01.tar.gz,nt.02.tar.gzI don't know the differents among these files ,and I don't which one I should choose to download.In addition ,I can't find the index file for phiX174. Could anyone help me and give me some advice please? Thank you very much. shenwiyn___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] tool shed can't install via admin user
Hi, I want to install our local Galaxy for more than one users. When I want to install some tools from tool shed via admin user ,and I followed the instructions in the follow link: http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#Installing_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance but these are some errors: Server Error URL: http://183.62.232.129:8081/galaxy/admin_toolshed/prepare_for_install?tool_shed_url=http://toolshed.g2.bx.psu.edu/repository_ids=1ec48b84b33d36d8changeset_revisions=41bba3e648d1 Module paste.exceptions.errormiddleware:143 in __call__ app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs ) Module galaxy.web.framework:208 in decorator return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.admin_toolshed:1177 in prepare_for_install response = urllib2.urlopen( url ) Module urllib2:126 in urlopen return _opener.open(url, data, timeout) Module urllib2:391 in open response = self._open(req, data) Module urllib2:409 in _open '_open', req) Module urllib2:369 in _call_chain result = func(*args) Module urllib2:1172 in http_open return self.do_open(httplib.HTTPConnection, req) Module urllib2:1147 in do_open raise URLError(err) Could anyone tell me why ,and how to solve? Thanks shenwiyn___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Tools and Data
Hi, I've installed Galaxy in local as what Rafael does.I want to make sure that the basic functions work successfully just depending on the necessary tools in Tool dependencies manual,and the NGS tools not only depend on the necessary tools but also some another needed data(such as indexes,and so on). thakks shenwy___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] all the data files in .loc files needed to download ?
Hi everyone, Thank you very much for your help. I want to download the complete directory of galaxy data through rsync -avzP rsync://datacache.g2.bx.psu.edu/indexes/phiX.But It can't work. And then I try to via http://dan.g2.bx.psu.edu/ by http://datacache.g2.bx.psu.edu/ ,I get 502 Bad Gateway. So what happens? How cat I get the data? Is there another way? Help me please. shenwiyn From: Carl Eberhard Date: 2013-02-27 22:28 To: Ross CC: shenwiyn; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello, Ross makes an important point: if this installation is for more than one user, you should install a more complete database system. This page may help with your decisions there: http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=showredirect=Admin%2FConfig%2FPerformance To your first question Is all the data in datacache.g2.bx.psu.edu/indexes needed?, I would say you should only need the data specific to the subject of your analyses and the tools you plan to use. To your second question can all of these needed data be downloaded (via rsync)? - perhaps you can clarify, please? We don't have any restriction on the amount you rsync from there and you're free to download all the data. If a problem or topic isn't covered in that wiki page, this mailing list is a good place to ask questions related to data set up. Thanks, Carl On Wed, Feb 27, 2013 at 5:44 AM, Ross ross.laza...@gmail.com wrote: Hi, shenwiyn I'd also add: Fourth, replace distributed default sqlite with postgresql to your list if it's for any serious use. Sqlite is ok for testing. On Wed, Feb 27, 2013 at 9:37 PM, shenwiyn shenw...@gmail.com wrote: Hello Carl, Thank you very much for your help.I have some thoughts about installing my local galaxy : First,download the latest source of galaxy from https://bitbucket.org/galaxy/galaxy-dist/ ,then install it in my local computer. Second,install dependencies tools mentioned in http://wiki.galaxyproject.org/Admin/Data%20Integration successfully. Third ,install the needed data and configure the .loc files from the following help of wiki page http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup. Finally ,our installation of local galaxy overs and it works in the mass.Is it right ? And I also have some confusions: First ,How large the total needed data is ?Is all the data in datacache.g2.bx.psu.edu/indexes needed ? Second, can all of these needed data be downloaded (via rsync) by the help of http://wiki.galaxyproject.org/Admin/Data%20Integration? These are the most important questions I concerned about now.I am so thankful for some of you advice. Thank you very much. shenwiyn From: Carl Eberhard Date: 2013-02-23 02:42 To: shenwiyn CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello shenwiyn, You may want to have a look at http://wiki.galaxyproject.org/Admin/Data%20Integration which provides more information specific to the indeces/data you'll need and how to install. Along with data management, that page has instructions on how to download (via rsync) the same data we use on our main server. It may be a good starting point. Thanks, Carl On Thu, Feb 21, 2013 at 8:58 PM, shenwiyn shenw...@foxmail.com wrote: Hi Carl Eberhard, Thank you very much for you help.I have another some questions : First, we need to install the needed data,for example sam_fa_indices.loc file of SAM Tools : index AaegL1 /afs/bx.psu.edu/depot/data/genome/AaegL1/sam_index/AaegL1.fa index AgamP3 /afs/bx.psu.edu/depot/data/genome/AgamP3/sam_index/AgamP3.fa index ailMel1 /afs/bx.psu.edu/depot/data/genome/ailMel1/sam_index/ailMel1.fa index anoCar2 /afs/bx.psu.edu/depot/data/genome/anoCar2/sam_index/anoCar2.fa index apiMel2 /afs/bx.psu.edu/depot/data/genome/apiMel2/sam_index/apiMel2.fa index apiMel3 /afs/bx.psu.edu/depot/data/genome/apiMel3/sam_index/apiMel3.fa index aplCal1 /afs/bx.psu.edu/depot/data/genome/aplCal1/sam_index/aplCal1.fa so we need to download AaegL1.fa,AgamP3.fa,ailMel1.fa,anoCar2.fa,apiMel2.fa,apiMel3.fa,and so on ,then install all of this needed datas to /afs/bx.psu.edu/depot/data/genome/aplCal1/sam_index/,is it right? Second, from the needed datas mentioned in the .loc files in http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup ,we need to download too much data,can we get all these data from some website instead of searching them on Iternet one by one? Thanks, shenwiyn From: Carl Eberhard Date: 2013-02-22 01:20 To: shenwiyn Subject: Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello, Yes a local galaxy requires a few steps in order to install the needed data. The following wiki page should help get you started: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Let me know if you need more information, Carl On Tue, Feb
Re: [galaxy-dev] all the data files in .loc files needed to download ?
Hello Carl, Thank you very much for your help.I have some thoughts about installing my local galaxy : First,download the latest source of galaxy from https://bitbucket.org/galaxy/galaxy-dist/ ,then install it in my local computer. Second,install dependencies tools mentioned in http://wiki.galaxyproject.org/Admin/Data%20Integration successfully. Third ,install the needed data and configure the .loc files from the following help of wiki page http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup. Finally ,our installation of local galaxy overs and it works in the mass.Is it right ? And I also have some confusions: First ,How large the total needed data is ?Is all the data in datacache.g2.bx.psu.edu/indexes needed ? Second, can all of these needed data be downloaded (via rsync) by the help of http://wiki.galaxyproject.org/Admin/Data%20Integration? These are the most important questions I concerned about now.I am so thankful for some of you advice. Thank you very much. shenwiyn From: Carl Eberhard Date: 2013-02-23 02:42 To: shenwiyn CC: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello shenwiyn, You may want to have a look at http://wiki.galaxyproject.org/Admin/Data%20Integration which provides more information specific to the indeces/data you'll need and how to install. Along with data management, that page has instructions on how to download (via rsync) the same data we use on our main server. It may be a good starting point. Thanks, Carl On Thu, Feb 21, 2013 at 8:58 PM, shenwiyn shenw...@foxmail.com wrote: Hi Carl Eberhard, Thank you very much for you help.I have another some questions : First, we need to install the needed data,for example sam_fa_indices.loc file of SAM Tools : index AaegL1 /afs/bx.psu.edu/depot/data/genome/AaegL1/sam_index/AaegL1.fa index AgamP3 /afs/bx.psu.edu/depot/data/genome/AgamP3/sam_index/AgamP3.fa index ailMel1 /afs/bx.psu.edu/depot/data/genome/ailMel1/sam_index/ailMel1.fa index anoCar2 /afs/bx.psu.edu/depot/data/genome/anoCar2/sam_index/anoCar2.fa index apiMel2 /afs/bx.psu.edu/depot/data/genome/apiMel2/sam_index/apiMel2.fa index apiMel3 /afs/bx.psu.edu/depot/data/genome/apiMel3/sam_index/apiMel3.fa index aplCal1 /afs/bx.psu.edu/depot/data/genome/aplCal1/sam_index/aplCal1.fa so we need to download AaegL1.fa,AgamP3.fa,ailMel1.fa,anoCar2.fa,apiMel2.fa,apiMel3.fa,and so on ,then install all of this needed datas to /afs/bx.psu.edu/depot/data/genome/aplCal1/sam_index/,is it right? Second, from the needed datas mentioned in the .loc files in http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup ,we need to download too much data,can we get all these data from some website instead of searching them on Iternet one by one? Thanks, shenwiyn From: Carl Eberhard Date: 2013-02-22 01:20 To: shenwiyn Subject: Re: [galaxy-dev] all the data files in .loc files needed to download ? Hello, Yes a local galaxy requires a few steps in order to install the needed data. The following wiki page should help get you started: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup Let me know if you need more information, Carl On Tue, Feb 19, 2013 at 3:59 AM, shenwiyn shenw...@gmail.com wrote: Hi all, Are all the data files in .loc files needed to download and put to the right directory when we install our local galaxy? thaks shenwiyn shenwiyn ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] all the data files in .loc files needed to download ?
Hi all, Are all the data files in .loc files needed to download and put to the right directory when we install our local galaxy? thaks shenwiyn shenwiyn___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
