Re: [galaxy-dev] How to set java heap size in Galaxy?
Hi Liu, if you set up your application in the XML to run with Java, like java -jar yourapplication.jar, it is sufficient to add the -Xmx parameter. Something like java -Xmx512m -jar yourapplication.jar Greets --- Marco On 27 June 2011 12:15, liu bo liub...@gmail.com wrote: Dear all, I have added an application to Galaxy's Tools. Now there occurs an error java.lang.OutOfMemoryError: Java heap space. Do you know how to set java heap size in Galaxy? Thank you very much. Best regards, Bo ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] postgresql connection error: could not connect to server: No such file or directory...
Hi Gus,
it seems that your postgres is not configured to accept connection except
localhost (or the deamon is not running). Did you try to connect to postgres
from another PC in the network (no the localhost)?
Did you install postgres using apt-get install? Do you run postgres using
/etc/init.d/postgresql-8.4 start?
Greets.
---
Marco
On 24 June 2011 21:52, W. Augustine Dunn III wadun...@gmail.com wrote:
Hello all:
Please forgive me if this is a matter of RTFM but I can assure you that I
have in fact TRIED that for a day or so now...
I am trying to set up a local GALAXY site for my lab so that I can start to
offload some of the work that comes my way as the sole biologist in our lab
not afraid of the command line. My system is Ubuntu 10.10 64b, i7 quad, 12
GB RAM. Since Multiple people will be using the site I decided to go with
the slightly more fancy postgresql db back-end rather than the sqlite
default. I had things running fine with the sqlite but can NOT seem to get
psql and galaxy to play nice.
I have created a galaxy role with rights to make tables on a created
galaxy database:
galaxy@vlad 12:40:20 ~/galaxy-dist:
psql
psql (8.4.8)
Type help for help.
galaxy= \l
List of databases
Name | Owner | Encoding | Collation | Ctype| Access
privileges
--+--+--+++---
galaxy | postgres | UTF8 | en_US.utf8 | en_US.utf8 |
=Tc/postgres
:
postgres=CTc/postgres
:
galaxy=CTc/postgres
postgres | postgres | UTF8 | en_US.utf8 | en_US.utf8 |
template0| postgres | UTF8 | en_US.utf8 | en_US.utf8 | =c/postgres
:
postgres=CTc/postgres
template1| postgres | UTF8 | en_US.utf8 | en_US.utf8 | =c/postgres
:
postgres=CTc/postgres
zabbix_proxy | postgres | UTF8 | en_US.utf8 | en_US.utf8 |
(5 rows)
I created a PGDATA file at /var/lib/postgresql/8.4/main/PGDATA and export a
PGDATA envar upon loading of the galaxy user's .bashrc pointing to this
place. I am able to start and stop the server with the postgres user using
pg_ctl. Once its running, I change users back to galaxy and try to run
run.sh and get the following traceback:
Traceback (most recent call last):
File /home/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py, line 82, in
app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File /home/galaxy/galaxy-dist/lib/galaxy/app.py, line 32, in __init__
create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get(
'__file__', None ), self.config.database_engine_options )
File /home/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py, line
54, in create_or_verify_database
dataset_table = Table( dataset, meta, autoload=True )
File
/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py,
line 108, in __call__
return type.__call__(self, name, metadata, *args, **kwargs)
File
/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/schema.py,
line 236, in __init__
_bind_or_error(metadata).reflecttable(self,
include_columns=include_columns)
File
/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py,
line 1261, in reflecttable
conn = self.contextual_connect()
File
/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/threadlocal.py,
line 194, in contextual_connect
return self.session.get_connection(**kwargs)
File
/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/threadlocal.py,
line 20, in get_connection
return self.engine.TLConnection(self, self.engine.pool.connect(),
close_with_result=close_with_result)
File
/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py,
line 151, in connect
agent = _ConnectionFairy(self)
File
/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py,
line 304, in __init__
rec = self._connection_record = pool.get()
File
/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py,
line 161, in get
return self.do_get()
File
/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py,
line 639, in do_get
con = self.create_connection()
File
/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py,
line 122, in create_connection
return _ConnectionRecord(self)
File
/home/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/pool.py,
line 198, in __init__
self.connection =
Re: [galaxy-dev] rpy and R
Hi Ryan, it seems like your compiler can't find the R header files. I don't know on which linux distro your're running Galaxy and if you installed with a package manager it or compiled it, but you should try to install R headers (the development packages). For example in Ubuntu an apt-get install r-base-dev should fix the problem. Hope it helps. --- Marco On 22 June 2011 01:43, Ryan Davis rrda...@ucdavis.edu wrote: Hi all, I'm currently working on setting up a Galaxy on our local server. I'm going through the tool dependencies list and install everything on it. I installed the latest R version (2.12.2) and now I'm trying to install rpy 1.0.3. I have installed R with --enable-R-shlib and also done this step: export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/R/lib/ However I get the following error with the install of rpy 1.0.3. Thanks for the help, Ryan [cgtepper@hobbes rpy-1.0.3]$ python setup.py install RHOMES= [] DEBUG= True Setting RHOMES to ['/usr/lib64/R'] ### Using R verion 2.12.2 installed at /usr/lib64/R ### RHOME= /usr/lib64/R copying src/rpymodule.c - src/rpymodule2122.c copying src/R_eval.c - src/R_eval2122.c copying src/io.c - src/io2122.c running install running build running build_py running build_ext building '_rpy2122' extension gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DRPY_SHNAME=_rpy2122 -DINIT_RPY=init_rpy2122 -UPRE_2_2 -UWITH_NUMERIC -I/usr/lib64/R/include -Isrc -I/usr/share/R/include -I/usr/local/include/python2.6 -c src/rpymodule2122.c -o build/temp.linux-x86_64-2.6/src/rpymodule2122.o -shared src/rpymodule2122.c:42:23: error: Rversion.h: No such file or directory src/rpymodule2122.c:43:28: error: missing binary operator before token ( In file included from src/rpymodule2122.c:51: src/RPy.h:51:15: error: R.h: No such file or directory src/RPy.h:52:22: error: Rdefines.h: No such file or directory src/RPy.h:53:24: error: Rinternals.h: No such file or directory src/RPy.h:57:28: error: R_ext/Rdynload.h: No such file or directory src/RPy.h:58:29: error: R_ext/eventloop.h: No such file or directory In file included from src/RPy.h:71, from src/rpymodule2122.c:51: src/rpy_Rinterface.h:51:27: error: R_ext/Boolean.h: No such file or directory In file included from src/rpy_Rinterface.h:61, from src/RPy.h:71, from src/rpymodule2122.c:51: src/rpy_Startup.h:70: error: expected specifier-qualifier-list before ‘Rboolean’ In file included from src/RPy.h:71, from src/rpymodule2122.c:51: src/rpy_Rinterface.h:70: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_Interactive’ src/rpy_Rinterface.h:71: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_Quiet’ src/rpy_Rinterface.h:72: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_Slave’ src/rpy_Rinterface.h:73: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘R_Verbose’ src/rpy_Rinterface.h:76: error: expected declaration specifiers or ‘...’ before ‘Rboolean’ src/rpy_Rinterface.h:85: warning: function declaration isn’t a prototype src/rpy_Rinterface.h:96: warning: function declaration isn’t a prototype src/rpy_Rinterface.h:101: warning: function declaration isn’t a prototype src/rpy_Rinterface.h:102: warning: function declaration isn’t a prototype src/rpy_Rinterface.h:103: warning: function declaration isn’t a prototype src/rpy_Rinterface.h:112: warning: parameter names (without types) in function declaration In file included from src/rpymodule2122.c:51: src/RPy.h:77:51: error: Rdevices.h: No such file or directory In file included from src/RPy.h:108, from src/rpymodule2122.c:51: src/robjobject.h:47: error: expected specifier-qualifier-list before ‘SEXP’ src/robjobject.h:62: error: expected ‘)’ before ‘int’ In file included from src/rpymodule2122.c:51: src/RPy.h:115: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘to_Robj’ src/RPy.h:116: warning: parameter names (without types) in function declaration src/RPy.h:117: warning: parameter names (without types) in function declaration src/RPy.h:118: error: expected ‘)’ before ‘int’ src/RPy.h:129: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘do_eval_expr’ src/RPy.h:130: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘do_eval_fun’ src/RPy.h:131: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘get_fun_from_name’ src/RPy.h:208: error: expected ‘)’ before ‘robj’ src/RPy.h:209: error: expected ‘)’ before ‘robj’ src/RPy.h:210: error: expected ‘)’ before ‘robj’ src/RPy.h:211: error: expected ‘)’ before ‘robj’ src/rpymodule2122.c:77: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘get_item’ src/rpymodule2122.c:78: error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘set_item’ src/rpymodule2122.c:79: error: expected ‘=’, ‘,’, ‘;’,
Re: [galaxy-dev] Galaxy tools written in java
Hi Frederick, I'm not an expert but maybe you could consider to write a python wrapper to call your Java application. --- Marco On 7 May 2011 08:08, Frederick van Staden cmptrwiz...@gmail.com wrote: Hello! Im looking for a way to run jar files(or class files) as a tool. Im not sure how to setup the galaxy instance to do this. For some reason i am running into a classpath issue. Anyone that could guide me in the right direction? Regards Frederick ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Problem downloading file from local Galaxy
Hi Nate, thanks for answering. I performed some tests stealing PCs from my collegues and actually it was a problem of my profile data. I experienced these problems with both Chromium and Firefox on my machine, but with others it works, so I decided to simply clean up my profile data and now it works also for me. Still don't know on what it could depend but in the end it doesn't really matter. The trick works. Thanks a lot. --- Marco On 6 May 2011 16:37, Nate Coraor n...@bx.psu.edu wrote: Marco Moretto wrote: Hi all, I successfully installed a Galaxy instance locally. I use Galaxy with Apache. Every time I try to download a file from history (like Options - Export to file) the browser (Firefox 3.6) reply with the error /tmp/lFeL6erm.asc.part could not be saved, because the source file could not be read.. I can correctly view the file content with the Display data in browser button. Thank you for any help. Hi Marco, Does this also happen with the single history item floppy disk icon? Are you using the sendfile module for Apache (described in the ApacheProxy page in our wiki)? Thanks, --nate --- Marco ___ 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] Problem with Torque/Maui
Hi all, first of all, thanks to the Galaxy Team for this really useful software. Actually I don't really know if my problem is related with Galaxy or with Torque/Maui but I didn't find any solution looking in both Torque and Maui user lists, so I hope that some of you with more experience could give me some good advices. I'm trying to set up Galaxy in a small local virtual environment in order to test it. I started with 2 virtual ubuntu servers called galaxy1 and galaxy2. On galaxy1 I succesfully installed Galaxy, Apache, Torque and Maui. I'm using Postgres ad DBMS. It is installed on another real DB server. The virtual server galaxy2 is used as node. Galaxy is working like a charm locally but when I try to use Torque problems arise. Torque alone works correctly. That means that I can submit a job with qsub and everything works. The 2 virtual server (galaxy1 and galaxy2) share a directory (through NFS) in which I installed Galaxy following the unified method from the documentation. Now, as I said, Galaxy alone works, Torque/Maui alone works. When I put the two together nothing works. As a test I upload (using local runner) a gff file. Then I try to make a filter to the gff using Filter and sort - Extract features. When I run this tool the corresponding job on the Torque queue runs forever in Hold state. I report some output from diagnose programs: The diagnose -j reports the following: Name State Par Proc QOS WCLimit R Min User Group Account QueuedTime Network Opsys ArchMem Disk Procs Class Features 29 Hold DEF1 DEF 1:00:00 01 galaxy galaxy-00:02:36 [NONE] [NONE] [NONE]=0=0NC0 [batch:1] [NONE] While the showq command reports ACTIVE JOBS JOBNAMEUSERNAME STATE PROC REMAINING STARTTIME 0 Active Jobs 0 of1 Processors Active (0.00%) IDLE JOBS-- JOBNAMEUSERNAME STATE PROC WCLIMIT QUEUETIME 0 Idle Jobs BLOCKED JOBS JOBNAMEUSERNAME STATE PROC WCLIMIT QUEUETIME 29 galaxy Hold 1 1:00:00 Wed May 4 03:56:40 The checkjob reports: checking job 29 State: Hold Creds: user:galaxy group:galaxy class:batch qos:DEFAULT WallTime: 00:00:00 of 1:00:00 SubmitTime: Wed May 4 03:56:40 (Time Queued Total: 00:03:07 Eligible: 00:00:01) The qstat -f reports Job Id: 33.galaxy1.research.intra.ismaa.it Job_Name = 27_extract_features1_marco.more...@iasma.it Job_Owner = gal...@galaxy1.research.intra.ismaa.it job_state = W queue = batch server = galaxy1.research.intra.ismaa.it ctime = Wed May 4 04:56:36 2011 Error_Path = galaxy1:/mnt/equallogic1/galaxy/galaxy-dist/database/pbs/27.e exec_host = galaxy2/0 exec_port = 15003 Execution_Time = Wed May 4 05:26:41 2011 mtime = Wed May 4 04:56:37 2011 Output_Path = galaxy1:/mnt/equallogic1/galaxy/galaxy-dist/database/pbs/27. o qtime = Wed May 4 04:56:36 2011 Resource_List.neednodes = 1 Resource_List.nodect = 1 Resource_List.nodes = 1 Resource_List.walltime = 01:00:00 stagein = /mnt/equallogic1/galaxy/tmp/dataset_18.dat@galaxy1 :/mnt/equallog ic1/galaxy/galaxy-dist/database/files/000/dataset_18.dat, /mnt/equallogic1/galaxy/tmp/dataset_30.dat@galaxy1 :/mnt/equallogic1/g alaxy/galaxy-dist/database/files/000/dataset_30.dat stageout = /mnt/equallogic1/galaxy/galaxy-dist/database/files/000/dataset_ 30.dat@galaxy1 :/mnt/equallogic1/galaxy/galaxy-dist/database/files/000/ dataset_30.dat substate = 37 Variable_List = PBS_O_QUEUE=batch, PBS_O_HOST=galaxy1.research.intra.ismaa.it euser = galaxy egroup = galaxy hashname = 33.galaxy1.research.intra.ismaa.it queue_rank = 33 queue_type = E StartDate: -00:03:06 Wed May 4 03:56:41 Total Tasks: 1 Req[0] TaskCount: 1 Partition: DEFAULT Network: [NONE] Memory = 0 Disk = 0 Swap = 0 Opsys: [NONE] Arch: [NONE] Features: [NONE] IWD: [NONE] Executable: [NONE] Bypass: 0 StartCount: 1 PartitionMask: [ALL] PE: 1.00 StartPriority: 1 cannot select job 29 for partition DEFAULT (non-idle state 'Hold') and finally the tracejob reports /var/spool/torque/server_priv/accounting/20110504: Permission denied /var/spool/torque/mom_logs/20110504: No such file or directory /var/spool/torque/sched_logs/20110504: No such file or directory Job: 33.galaxy1.research.intra.ismaa.it 05/04/2011 04:56:36 Senqueuing into batch, state 1 hop 1 05/04/2011 04:56:36 SJob Queued at request of gal...@galaxy1.research.intra.ismaa.it, owner = gal...@galaxy1.research.intra.ismaa.it, job name = 27_extract_features1_marco.more...@iasma.it, queue = batch 05/04/2011 04:56:37 SJob Run at request of gal...@galaxy1.research.intra.ismaa.it 05/04/2011 04:56:41 SEmail 's' to
