[galaxy-dev] speed and large file question (after tying galaxy to Pittsburgh)
Hi, General: Is there a quantifiable difference in data uploads, speed of processing, general availability after the connection was/is established to Pittsburgh? Specific: If we loaded data to a common directory on an XSEDE resource, would our students be able to fetch this data in a more timely manner to their galaxy accounts then from desktops etc... For us it would be easy to populate a common directory once then our users could fetch/wget etc... from there, or if possible could such directory be directly visible to our set of galaxy users? (this is what we do locally) - but one would need admin priv for that on the main instance. Or would you just do this with one galaxy user sharing out the files for the rest of a group working together? thanks. joe ___ 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] Job output not returned from cluster
Ed, we had the classic goof on our cluster with this. 4 nodes could not see the /home/galaxy folder due to a missing entry in /etc/fstab. When the jobs hit those nodes (which explains the randomness) we got the error message. Bothersome was the lack of good logs to go on. The error message was too generic - however I discovered that Galaxy was depositing the error and our messages in the /pbs folder and you could briefly read them before they got deleted. There the message was the classic SGE input/output message - /home/galaxy file not found. Hence my follow up question - how can I have galaxy NOT to delete these SGE error and out files? best, joe From: Edward Kirton [eskir...@lbl.gov] Sent: Monday, November 28, 2011 4:15 PM To: Nate Coraor Cc: Joseph Hargitai; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Job output not returned from cluster hi, we've had this issue too -- in short, the cluster node(s) finish writing outfiles to disk, but the file system (inode metadata) isn't updated at the galaxy server yet when galaxy checks for the files. turning the metadata caching off (as recommended on the galaxy wiki) isn't an option for me (and the performance hit would be significant), so i added some loops around the file checking (5sec sleep and retry up to 6 times). there were a couple of places this probably should be done (not just .[eo]* log files but also the outfiles). i am testing these hacks now but due to the intermittent nature of these errors, it'll be a few days before i know if this is working as expected. once vetted, i will put these minor edits in a clone of galaxy-central so the changes can be picked up. ed On Mon, Oct 24, 2011 at 10:24 AM, Nate Coraor n...@bx.psu.edumailto:n...@bx.psu.edu wrote: Joseph Hargitai wrote: Nate, this error is intermittent. You resubmit the same job twice or three time and then it works. Once we are over the midterm exams - which use galaxy - we will try to switch the filesystem from autofs to hard mount. We suspect this to be the issue. Ah, I suspect this is attribute caching in NFS. Try mounting with the option 'noac' and see if it solves the problem. Could we suppress e and o SGE style to resolve this issue, or Galaxy wants the o? The filename is unimportant, but I doubt it's the cause. Do you have an idea about the url build for galaxy - ucsc page return when the url is :8080/galaxy and not just /galaxy? Not off the top of my head. I have this message marked, I'll take a look as soon as I have time. --nate thanks, joe From: Nate Coraor [n...@bx.psu.edumailto:n...@bx.psu.edu] Sent: Friday, October 21, 2011 10:26 AM To: Joseph Hargitai Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Job output not returned from cluster Joseph Hargitai wrote: Hi, i was browsing through the list and found many entries for this issue but not a definite answer. We are actually running into this error for simple file uploads from the internal filesystem. Hi Joe, This error occurs when the job's standard output and error files are not found where Galaxy expects them, namely: cluster_files_directory/job_id.o cluster_files_directory/job_id.e Please check your queueing system to make sure it can correctly deliver these back from the execution hosts to the specified filesystem. --nate thanks, joe ___ 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/ ___ 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] Job output not returned from cluster
Nate, this error is intermittent. You resubmit the same job twice or three time and then it works. Once we are over the midterm exams - which use galaxy - we will try to switch the filesystem from autofs to hard mount. We suspect this to be the issue. Could we suppress e and o SGE style to resolve this issue, or Galaxy wants the o? Do you have an idea about the url build for galaxy - ucsc page return when the url is :8080/galaxy and not just /galaxy? thanks, joe From: Nate Coraor [n...@bx.psu.edu] Sent: Friday, October 21, 2011 10:26 AM To: Joseph Hargitai Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Job output not returned from cluster Joseph Hargitai wrote: Hi, i was browsing through the list and found many entries for this issue but not a definite answer. We are actually running into this error for simple file uploads from the internal filesystem. Hi Joe, This error occurs when the job's standard output and error files are not found where Galaxy expects them, namely: cluster_files_directory/job_id.o cluster_files_directory/job_id.e Please check your queueing system to make sure it can correctly deliver these back from the execution hosts to the specified filesystem. --nate thanks, joe ___ 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] GALAXY_URL with port 8080
Hi, just noticed that in our current setup the baseurl to post data back from ucsc tablebrowser is not picking up the port designation. I looked at two files: ucsc_display_sites inputs action=http://genome-test.cse.ucsc.edu/cgi-bin/hgTables; check_values=false method=get displaygo to UCSC Table Browser $GALAXY_URL/display param name=GALAXY_URL type=baseurl value=/tool_runner / param name=tool_id type=hidden value=ucsc_table_direct_test1 / param name=sendToGalaxy type=hidden value=1 / param name=hgta_compressType type=hidden value=none / param name=hgta_outputType type=hidden value=bed / /inputs request_param_translation request_param galaxy_name=URL_method remote_name=URL_method missing=post / it looks like too late to modify this part. and in __init__.py can somewhere the GALAXY_URL or REDIRECT_URL to reflect http:/site.blah.edu:8000/galaxy versus what it does now http:/site.blah.edu/galaxy ? Where/home __init__.py picking up the wrong url here? If it is from the *.ini setting of cookie path and cookie - can that be set to :8080/galaxy ? thanks, joe ___ 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] moving the galaxy-dist folder structure
Ross, i am looking through three of our instances and none has any jar files in the /shared/jar/ folder. so it happens, i also cannot bring up a new cloud instance either to verify this issue. j From: Ross [ross.laza...@gmail.com] Sent: Thursday, October 13, 2011 11:19 PM To: Joseph Hargitai Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] moving the galaxy-dist folder structure Hi, Joe - not sure this will help but here goes: As you know, most tools expect to find normal executables (like bwa and samtools) on the execution host path but java packages like FastQC are a special case. Java based tool wrappers like the Picard tools expect to find the Picard jar files in [...]/tool-data/shared/jars FastQC is an even more particular case because there's a fastqc perl script which has to be in the same place as the fastqc java, so the Galaxy tool wrapper expects to find it inside a copy of the FastQC distribution inside a folder called [your galaxy root]/tool-data/shared/jars/FastQC. If you moved or recursively copied all of the subdirectories of your Galaxy root from one place to another (including tool-data/shared) everything should just continue to work unless there are permission problems? On Fri, Oct 14, 2011 at 10:21 AM, Joseph Hargitai joseph.hargi...@einstein.yu.edu wrote: Hi, we moved the /home/galaxy/galaxy-dist structure to another fs. Some tools, like fastqc, stopped working. Are there internal links that we possibly ignored? Is there a way to adjust the installation via a download or update? joe ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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] galaxy cloud install hangs
Hi, trying to bring up a new instance. 1, remove old cm from S3 bucket 2, bring up new 3, get console 4, SGE and fs running 5,Database and galaxy are not running 6, on /mnt i see /mnt and galaxyData East 1c xy Cloudman Admin | Report bugs | Wiki | Screencast Only up to the most recent 200 lines of the file (paster.log) are shown. Show all | Show less | Show more | Back to admin view [DEBUG] sge:311 2011-10-14 08:54:00,368: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.24 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:54:00,445: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:54:16,706: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.24 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:54:16,759: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:54:33,018: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.24 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:54:33,085: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:54:49,421: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.20 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:54:49,853: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:55:06,110: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.20 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:55:06,161: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:55:22,440: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.19 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:55:22,754: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:55:39,011: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.19 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:55:39,063: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:55:55,326: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.19 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:55:55,375: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:56:11,634: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.19 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:56:11,684: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:56:27,948: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.19 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:56:28,002: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:56:44,264: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.20 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:56:44,356: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:57:00,623: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.20 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:57:00,672: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:57:16,920: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.17 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:57:16,971: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:57:33,229: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.17 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:57:33,276: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:57:49,529: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.17 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:57:49,579: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:58:05,844: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.18 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:58:05,938: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:58:22,207: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.18 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:58:22,258: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:58:38,512: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.14 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:58:38,562: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:58:54,832: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.14 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:58:54,896: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:59:11,159: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.14 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:59:11,223: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:59:27,542: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.09 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:59:27,631: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14 08:59:43,920: qstat: ['al...@ip-10-191-205-72.ec2.int BIP 0/0/4 1.09 lx24-amd64'] [DEBUG] master:1510 2011-10-14 08:59:43,968: SS: SGE..OK; FS-galaxyData..OK; [DEBUG] sge:311 2011-10-14
[galaxy-dev] Job output not returned from cluster
Hi, i was browsing through the list and found many entries for this issue but not a definite answer. We are actually running into this error for simple file uploads from the internal filesystem. thanks, joe ___ 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] moving the galaxy-dist folder structure
Hi, we moved the /home/galaxy/galaxy-dist structure to another fs. Some tools, like fastqc, stopped working. Are there internal links that we possibly ignored? Is there a way to adjust the installation via a download or update? joe ___ 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] cloud instance missing /opt/sge/default/common directory
Hi, the mount is no longer there: ubuntu@ip-10-68-42-15:~$ more /etc/hosts 127.0.0.1 localhost # The following lines are desirable for IPv6 capable hosts ::1 ip6-localhost ip6-loopback fe00::0 ip6-localnet ff00::0 ip6-mcastprefix ff02::1 ip6-allnodes ff02::2 ip6-allrouters ff02::3 ip6-allhosts ubuntu@ip-10-68-42-15:~$ df -h FilesystemSize Used Avail Use% Mounted on /dev/sda1 15G 9.5G 5.6G 63% / devtmpfs 7.3G 128K 7.3G 1% /dev none 7.6G 0 7.6G 0% /dev/shm none 7.6G 96K 7.6G 1% /var/run none 7.6G 0 7.6G 0% /var/lock none 7.6G 0 7.6G 0% /lib/init/rw /dev/sdb 414G 201M 393G 1% /mnt ubuntu@ip-10-68-42-15:~$ cd /mnt ubuntu@ip-10-68-42-15:/mnt$ ls cm lost+found ubuntu@ip-10-68-42-15:/mnt$ more /etc/fstab # /etc/fstab: static file system information. # file system mount point type options dump pass proc/proc procnodev,no exec,nosuid 0 0 /dev/sda1 / xfs defaults 0 0 /dev/sdb/mntautodefaults,nobootwait,comment=cloudconfig0 0 From: Enis Afgan [eaf...@emory.edu] Sent: Thursday, September 22, 2011 8:48 AM To: Joseph Hargitai Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cloud instance missing /opt/sge/default/common directory Hi Joe, And this is happening on a freshly booted instance (from a previously existing cluster) using the same AMI? The order of execution seems a bit odd, seeing Galaxy being removed before SGE is setup; SGE should be the first thing that gets setup so I'm wondering... If you log into the instance, what is in /etc/hosts? Does it match the instance DNS? And if you try executing that same command (cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf) by hand (as root), is any more info produced? Also, qmaster log should be available under /opt/sge/ge6 (or something like this) /default/spool/qmaster/ so please take a look there as well and see if more info is available. On Thu, Sep 22, 2011 at 12:46 AM, Joseph Hargitai joseph.hargi...@einstein.yu.edumailto:joseph.hargi...@einstein.yu.edu wrote: the error is ' [DEBUG] galaxy:139 2011-09-22 00:03:21,055: Galaxy UI does not seem to be accessible. [DEBUG] master:1491 2011-09-22 00:03:21,055: SS: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] root:354 2011-09-22 00:03:24,724: Managing services: [] [INFO] galaxy:30 2011-09-22 00:03:24,724: Removing 'Galaxy' service [INFO] galaxy:122 2011-09-22 00:03:24,724: Shutting down Galaxy... [DEBUG] misc:511 2011-09-22 00:03:26,067: Successfully stopped Galaxy. [DEBUG] root:354 2011-09-22 00:03:33,936: Managing services: [] [DEBUG] sge:61 2011-09-22 00:03:33,937: Unpacking SGE from '/opt/galaxy/pkg/ge6.2u5' [DEBUG] sge:76 2011-09-22 00:03:33,937: Cleaning '/opt/sge' directory. [DEBUG] sge:82 2011-09-22 00:03:34,117: Unpacking SGE to '/opt/sge'. [INFO] sge:96 2011-09-22 00:03:35,557: Configuring SGE... [DEBUG] sge:104 2011-09-22 00:03:35,558: Created SGE install template as file '/opt/sge/galaxyEC2.conf' [DEBUG] sge:112 2011-09-22 00:03:35,558: Setting up SGE. [ERROR] misc:514 2011-09-22 00:03:35,651: Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '2' and following stderr: '[: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator error resolving local host: can't resolve host name (h_errno = HOST_NOT_FOUND) j From: Enis Afgan [afg...@gmail.commailto:afg...@gmail.com] Sent: Tuesday, September 13, 2011 4:20 AM To: Joseph Hargitai Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cloud instance missing /opt/sge/default/common directory Hi Joe, If you look in /mnt/cm/paster.log on the instance, are there any indications as to what went wrong? It should be toward the top of the log after the server gets started. SGE gets installed each time an instance is rebooted so simply rebooting it again may do the trick. You can also chose to manually remove/clean SGE before rebooting. To do so, you can follow the basic approach captured in this method: https://bitbucket.org/galaxy/cloudman/src/862d1087080f/cm/services/apps/sge.py#cl-26 Enis On Sun, Sep 11, 2011 at 12:05 AM, Joseph Hargitai joseph.hargi...@einstein.yu.edumailto:joseph.hargi...@einstein.yu.edu wrote: Hi, Upon restarting a saved cloud instance I am missing: -bash: /opt/sge/default/common/settings.sh: No such file or directory -bash: /opt/sge/default/common/settings.sh: No such file or directory all the other mounts
Re: [galaxy-dev] cloud instance missing /opt/sge/default/common directory
Hi, Correct. Same instance. Slowly deteriorating even more - at first it had only SGE and Galaxy hung. Now when rebooting, only CM starts. No fs, postgres... The knee-jerk reaction is to just start a brand new instance, but that would not help anyone who wants to use this AIM in the future for production. I'll check your recommendation shortly. j From: Enis Afgan [eaf...@emory.edu] Sent: Thursday, September 22, 2011 8:48 AM To: Joseph Hargitai Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cloud instance missing /opt/sge/default/common directory Hi Joe, And this is happening on a freshly booted instance (from a previously existing cluster) using the same AMI? The order of execution seems a bit odd, seeing Galaxy being removed before SGE is setup; SGE should be the first thing that gets setup so I'm wondering... If you log into the instance, what is in /etc/hosts? Does it match the instance DNS? And if you try executing that same command (cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf) by hand (as root), is any more info produced? Also, qmaster log should be available under /opt/sge/ge6 (or something like this) /default/spool/qmaster/ so please take a look there as well and see if more info is available. On Thu, Sep 22, 2011 at 12:46 AM, Joseph Hargitai joseph.hargi...@einstein.yu.edumailto:joseph.hargi...@einstein.yu.edu wrote: the error is ' [DEBUG] galaxy:139 2011-09-22 00:03:21,055: Galaxy UI does not seem to be accessible. [DEBUG] master:1491 2011-09-22 00:03:21,055: SS: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] root:354 2011-09-22 00:03:24,724: Managing services: [] [INFO] galaxy:30 2011-09-22 00:03:24,724: Removing 'Galaxy' service [INFO] galaxy:122 2011-09-22 00:03:24,724: Shutting down Galaxy... [DEBUG] misc:511 2011-09-22 00:03:26,067: Successfully stopped Galaxy. [DEBUG] root:354 2011-09-22 00:03:33,936: Managing services: [] [DEBUG] sge:61 2011-09-22 00:03:33,937: Unpacking SGE from '/opt/galaxy/pkg/ge6.2u5' [DEBUG] sge:76 2011-09-22 00:03:33,937: Cleaning '/opt/sge' directory. [DEBUG] sge:82 2011-09-22 00:03:34,117: Unpacking SGE to '/opt/sge'. [INFO] sge:96 2011-09-22 00:03:35,557: Configuring SGE... [DEBUG] sge:104 2011-09-22 00:03:35,558: Created SGE install template as file '/opt/sge/galaxyEC2.conf' [DEBUG] sge:112 2011-09-22 00:03:35,558: Setting up SGE. [ERROR] misc:514 2011-09-22 00:03:35,651: Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '2' and following stderr: '[: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator error resolving local host: can't resolve host name (h_errno = HOST_NOT_FOUND) j From: Enis Afgan [afg...@gmail.commailto:afg...@gmail.com] Sent: Tuesday, September 13, 2011 4:20 AM To: Joseph Hargitai Cc: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cloud instance missing /opt/sge/default/common directory Hi Joe, If you look in /mnt/cm/paster.log on the instance, are there any indications as to what went wrong? It should be toward the top of the log after the server gets started. SGE gets installed each time an instance is rebooted so simply rebooting it again may do the trick. You can also chose to manually remove/clean SGE before rebooting. To do so, you can follow the basic approach captured in this method: https://bitbucket.org/galaxy/cloudman/src/862d1087080f/cm/services/apps/sge.py#cl-26 Enis On Sun, Sep 11, 2011 at 12:05 AM, Joseph Hargitai joseph.hargi...@einstein.yu.edumailto:joseph.hargi...@einstein.yu.edu wrote: Hi, Upon restarting a saved cloud instance I am missing: -bash: /opt/sge/default/common/settings.sh: No such file or directory -bash: /opt/sge/default/common/settings.sh: No such file or directory all the other mounts are there and well preserved. Is this pulled from a special place i may have not saved? The instance now does not boot beyond this point. Have login and admin console access. joe ___ 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] cloud instance missing /opt/sge/default/common directory
the error is ' [DEBUG] galaxy:139 2011-09-22 00:03:21,055: Galaxy UI does not seem to be accessible. [DEBUG] master:1491 2011-09-22 00:03:21,055: SS: SGE..Shut down; FS-galaxyIndices..OK; FS-galaxyTools..OK; FS-galaxyData..OK; Postgres..OK; Galaxy..Starting; [DEBUG] root:354 2011-09-22 00:03:24,724: Managing services: [] [INFO] galaxy:30 2011-09-22 00:03:24,724: Removing 'Galaxy' service [INFO] galaxy:122 2011-09-22 00:03:24,724: Shutting down Galaxy... [DEBUG] misc:511 2011-09-22 00:03:26,067: Successfully stopped Galaxy. [DEBUG] root:354 2011-09-22 00:03:33,936: Managing services: [] [DEBUG] sge:61 2011-09-22 00:03:33,937: Unpacking SGE from '/opt/galaxy/pkg/ge6.2u5' [DEBUG] sge:76 2011-09-22 00:03:33,937: Cleaning '/opt/sge' directory. [DEBUG] sge:82 2011-09-22 00:03:34,117: Unpacking SGE to '/opt/sge'. [INFO] sge:96 2011-09-22 00:03:35,557: Configuring SGE... [DEBUG] sge:104 2011-09-22 00:03:35,558: Created SGE install template as file '/opt/sge/galaxyEC2.conf' [DEBUG] sge:112 2011-09-22 00:03:35,558: Setting up SGE. [ERROR] misc:514 2011-09-22 00:03:35,651: Setting up SGE did not go smoothly, running command 'cd /opt/sge; ./inst_sge -m -x -auto /opt/sge/galaxyEC2.conf' returned code '2' and following stderr: '[: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator [: 359: 11: unexpected operator error resolving local host: can't resolve host name (h_errno = HOST_NOT_FOUND) j From: Enis Afgan [afg...@gmail.com] Sent: Tuesday, September 13, 2011 4:20 AM To: Joseph Hargitai Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] cloud instance missing /opt/sge/default/common directory Hi Joe, If you look in /mnt/cm/paster.log on the instance, are there any indications as to what went wrong? It should be toward the top of the log after the server gets started. SGE gets installed each time an instance is rebooted so simply rebooting it again may do the trick. You can also chose to manually remove/clean SGE before rebooting. To do so, you can follow the basic approach captured in this method: https://bitbucket.org/galaxy/cloudman/src/862d1087080f/cm/services/apps/sge.py#cl-26 Enis On Sun, Sep 11, 2011 at 12:05 AM, Joseph Hargitai joseph.hargi...@einstein.yu.edumailto:joseph.hargi...@einstein.yu.edu wrote: Hi, Upon restarting a saved cloud instance I am missing: -bash: /opt/sge/default/common/settings.sh: No such file or directory -bash: /opt/sge/default/common/settings.sh: No such file or directory all the other mounts are there and well preserved. Is this pulled from a special place i may have not saved? The instance now does not boot beyond this point. Have login and admin console access. joe ___ 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] cloud instance missing /opt/sge/default/common directory
Hi, Upon restarting a saved cloud instance I am missing: -bash: /opt/sge/default/common/settings.sh: No such file or directory -bash: /opt/sge/default/common/settings.sh: No such file or directory all the other mounts are there and well preserved. Is this pulled from a special place i may have not saved? The instance now does not boot beyond this point. Have login and admin console access. joe ___ 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] rpy - No module named rpy CentoOs install
Nate, could we go to the beginning of the issue: where is the galaxy env set? I've seen a few post but I can only gather partial info. - it is NOT set from the galaxy user .bashrc or .profile - if it is indeed partially set from /etc/profile - using a Rocks cluster leaves you with many entries there to ponder - if it is using ld.so.conf.d as well - it will read /usr/lib64 entries etc... - is there a precise way to see what env is used for galaxy? The log script gives you a nice read on the python path but is there a way to see all envs? Looking at envs as the user galaxy does not equate what galaxy ends up using. multiple issues on the CentOS install: I found the setting or non-setting leading to the missing rpy module by looking at the runner log script - while it was loading python2.6.6 it was also loading the site-packages and other python parts from /usr/lib64...python2.4 Once I edited run.sh to use the correct python and correct R path and added the RHOME to the rpy dependent scripts - this problem went away seemingly only to produce an env looking issue: sh rm command not found when running rpy dependent applications. Did somehow the edit destroy the /bin and usr/bin path? Would these be set in run.sh as well? To your question: where do you set RHOME in the env? We'd prefer to set all path options in run.sh in case all above is true that you cannot set it in ~/.bash* best, joe From: Nate Coraor [n...@bx.psu.edu] Sent: Friday, September 02, 2011 1:40 PM To: Joseph Hargitai Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] rpy - No module named rpy CentoOs install Joseph Hargitai wrote: additional info: it is possible on the same node to run manually ./gsummary.py with the header: #!/usr/bin/env python import sys, re, tempfile from rpy_options import set_options set_options(RHOME='/apps1/R/2.13.1/intel/lib64/R') from rpy import * Where else can there be an env setting to prevent this app not finding the mod from within galaxy? Hi Joe, If you set RHOME in the environment and then run gsummary.py without the additions, does it work? --nate j From: Joseph Hargitai Sent: Thursday, September 01, 2011 12:28 PM To: galaxy-dev@lists.bx.psu.edu Subject: rpy - No module named rpy CentoOs install Hi, On our Ubuntu install stat packages and all that require rpy work fine. On our CentOs install seeing this stubborn error that I did see from previous post to be difficult to fix. At first suspected the SGE issue - environment not transferring to compute nodes. After changing the app to run local had the same issue. CentOs: 2.6.18-92.1.13.el5 rpy module is in: /apps1/python/2.6.6/intel/lib/python2.6/site-packages _rpy2122.so _rpy2131.so version: [galaxy@compute-0-65 galaxy-dist]$ python -c import rpy; print rpy.__version__ 1.5.1 path: python -c 'import sys; print \n.join( sys.path )' /apps1/python/2.6.6/intel/lib/python2.6/site-packages/simplejson-2.0.9-py2.6-linux-x86_64.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Sphinx-1.0.7-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/docutils-0.7-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Jinja2-2.5.5-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Pygments-1.4-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/nose-1.0.0-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Traits-3.5.0-py2.6-linux-x86_64.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/nibabel-1.0.0-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/nipype-0.0.0-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/setuptools-0.6c12dev_r88846-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/birdsuite-1.0-py2.5.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/mpgutils-0.7-py2.5.egg /apps1/python/2.6.6/intel/lib/python26.zip /apps1/python/2.6.6/intel/lib/python2.6 /apps1/python/2.6.6/intel/lib/python2.6/plat-linux2 /apps1/python/2.6.6/intel/lib/python2.6/lib-tk /apps1/python/2.6.6/intel/lib/python2.6/lib-old /apps1/python/2.6.6/intel/lib/python2.6/lib-dynload /apps1/python/2.6.6/intel/lib/python2.6/site-packages /apps1/python/2.6.6/intel/lib/python2.6/site-packages/PIL compiled against /R/2.13.1 env: export PATH=.:\ /apps1/R/2.13.1/intel/bin:\ /apps1/python/2.6.6/intel/bin:\ /apps1/pipe/bowtie/0.12.7/intel:\ /apps1/pipe/bwa/0.5.9/intel:\ /apps1/samtools/0.1.13/intel/bin:\ /apps1/fastx_toolkit/0.0.13/intel/bin:\ /apps1/maq/maq-0.7.1:\ /apps1/maq/maq-0.7.1/scripts:\ /apps1/bfast/bfast-0.6.5a/butil:\ /apps1/bfast/bfast-0.6.5a/scripts:\ /apps1/abyss/1.2.7/intel/bin:\ /apps1/velvet/velvet_1.0.12:\ /apps1/pipe/tophat/1.3.0/intel/bin:\ /apps1/pipe/cufflinks/1.0.3/intel/bin:\ /apps1/blast/2.2.25/gnu/bin:\ /apps1/blast+/2.2.5/gnu/bin:\ /apps1/sputnik
[galaxy-dev] rpy - No module named rpy CentoOs install
Hi, On our Ubuntu install stat packages and all that require rpy work fine. On our CentOs install seeing this stubborn error that I did see from previous post to be difficult to fix. At first suspected the SGE issue - environment not transferring to compute nodes. After changing the app to run local had the same issue. CentOs: 2.6.18-92.1.13.el5 rpy module is in: /apps1/python/2.6.6/intel/lib/python2.6/site-packages _rpy2122.so _rpy2131.so version: [galaxy@compute-0-65 galaxy-dist]$ python -c import rpy; print rpy.__version__ 1.5.1 path: python -c 'import sys; print \n.join( sys.path )' /apps1/python/2.6.6/intel/lib/python2.6/site-packages/simplejson-2.0.9-py2.6-linux-x86_64.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Sphinx-1.0.7-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/docutils-0.7-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Jinja2-2.5.5-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Pygments-1.4-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/nose-1.0.0-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Traits-3.5.0-py2.6-linux-x86_64.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/nibabel-1.0.0-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/nipype-0.0.0-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/setuptools-0.6c12dev_r88846-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/birdsuite-1.0-py2.5.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/mpgutils-0.7-py2.5.egg /apps1/python/2.6.6/intel/lib/python26.zip /apps1/python/2.6.6/intel/lib/python2.6 /apps1/python/2.6.6/intel/lib/python2.6/plat-linux2 /apps1/python/2.6.6/intel/lib/python2.6/lib-tk /apps1/python/2.6.6/intel/lib/python2.6/lib-old /apps1/python/2.6.6/intel/lib/python2.6/lib-dynload /apps1/python/2.6.6/intel/lib/python2.6/site-packages /apps1/python/2.6.6/intel/lib/python2.6/site-packages/PIL compiled against /R/2.13.1 env: export PATH=.:\ /apps1/R/2.13.1/intel/bin:\ /apps1/python/2.6.6/intel/bin:\ /apps1/pipe/bowtie/0.12.7/intel:\ /apps1/pipe/bwa/0.5.9/intel:\ /apps1/samtools/0.1.13/intel/bin:\ /apps1/fastx_toolkit/0.0.13/intel/bin:\ /apps1/maq/maq-0.7.1:\ /apps1/maq/maq-0.7.1/scripts:\ /apps1/bfast/bfast-0.6.5a/butil:\ /apps1/bfast/bfast-0.6.5a/scripts:\ /apps1/abyss/1.2.7/intel/bin:\ /apps1/velvet/velvet_1.0.12:\ /apps1/pipe/tophat/1.3.0/intel/bin:\ /apps1/pipe/cufflinks/1.0.3/intel/bin:\ /apps1/blast/2.2.25/gnu/bin:\ /apps1/blast+/2.2.5/gnu/bin:\ /apps1/sputnik/intel/bin:\ /apps1/taxonomy/intel/bin:\ /apps1/add_scores/add_scores:\ /apps1/emboss/6.4.0/intel/bin:\ /apps1/hyphy/hyphy/HYPHY:\ /apps1/lastz/1.02.00:\ /apps1/perm/0.3.6/intel/bin:\ /apps1/beam2/intel/bin:\ /apps1/pass2/intel/bin:\ /apps1/plink/1.07/intel/bin:\ /apps1/fbat/2.0.3/bin:\ /apps1/eigensoft/3.0/intel/bin:\ /apps1/mosaik/Mosaik-1.1.0021-Linux-x64/bin:\ /apps1/freebayes/freebayes.git/bin:\ $PATH export LD_LIBRARY_PATH=.:\ /apps1/python/2.6.6/intel/lib:\ /apps1/libgtextutils/0.6/intel/lib:\ /apps1/emboss/6.4.0/intel/lib:\ /apps1/intel/lib/intel64:\ /apps1/intel/mkl/lib/em64t:\ /apps1/tcltk/8.5.9/intel/lib:\ /apps1/zlib/1.2.5/intel/lib:\ /apps1/graphviz/2.26.3/intel/lib:\ /apps1/python/2.6.6/intel/lib/python2.6/site-packages/simtk/chem/openmm/OpenMM:\ /apps1/python/2.6.6/intel/lib/python2.6/site-packages:\ /apps1/libpng/1.5.0/intel/lib:\ /apps1/R/2.13.1/intel/lib64/R/lib:\ $LD_LIBRARY_PATH export PKG_CONFIG_PATH=.:\ /apps1/R/2.13.1/intel/lib64/pkgconfig:\ /apps1/libgtextutils/0.6/intel/lib/pkgconfig:\ /apps1/sparsehash/1.11/intel/lib/pkgconfig:\ $PKG_CONFIG_PATH export CLASSPATH=.:\ /apps1/gatk/gatk-git/dist:\ /apps1/gatk/gatk-git/lib:\ /apps1/srma/srma-0.1.13:\ /apps1/haploview/4.2:\ /apps1/picard/picard-tools-1.50:\ /apps1/fastqc/fastqc-0.9.5:\ $CLASSPATH best, joe ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] rpy - No module named rpy CentoOs install
additional info: it is possible on the same node to run manually ./gsummary.py with the header: #!/usr/bin/env python import sys, re, tempfile from rpy_options import set_options set_options(RHOME='/apps1/R/2.13.1/intel/lib64/R') from rpy import * Where else can there be an env setting to prevent this app not finding the mod from within galaxy? j From: Joseph Hargitai Sent: Thursday, September 01, 2011 12:28 PM To: galaxy-dev@lists.bx.psu.edu Subject: rpy - No module named rpy CentoOs install Hi, On our Ubuntu install stat packages and all that require rpy work fine. On our CentOs install seeing this stubborn error that I did see from previous post to be difficult to fix. At first suspected the SGE issue - environment not transferring to compute nodes. After changing the app to run local had the same issue. CentOs: 2.6.18-92.1.13.el5 rpy module is in: /apps1/python/2.6.6/intel/lib/python2.6/site-packages _rpy2122.so _rpy2131.so version: [galaxy@compute-0-65 galaxy-dist]$ python -c import rpy; print rpy.__version__ 1.5.1 path: python -c 'import sys; print \n.join( sys.path )' /apps1/python/2.6.6/intel/lib/python2.6/site-packages/simplejson-2.0.9-py2.6-linux-x86_64.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Sphinx-1.0.7-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/docutils-0.7-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Jinja2-2.5.5-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Pygments-1.4-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/nose-1.0.0-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/Traits-3.5.0-py2.6-linux-x86_64.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/nibabel-1.0.0-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/nipype-0.0.0-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/setuptools-0.6c12dev_r88846-py2.6.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/birdsuite-1.0-py2.5.egg /apps1/python/2.6.6/intel/lib/python2.6/site-packages/mpgutils-0.7-py2.5.egg /apps1/python/2.6.6/intel/lib/python26.zip /apps1/python/2.6.6/intel/lib/python2.6 /apps1/python/2.6.6/intel/lib/python2.6/plat-linux2 /apps1/python/2.6.6/intel/lib/python2.6/lib-tk /apps1/python/2.6.6/intel/lib/python2.6/lib-old /apps1/python/2.6.6/intel/lib/python2.6/lib-dynload /apps1/python/2.6.6/intel/lib/python2.6/site-packages /apps1/python/2.6.6/intel/lib/python2.6/site-packages/PIL compiled against /R/2.13.1 env: export PATH=.:\ /apps1/R/2.13.1/intel/bin:\ /apps1/python/2.6.6/intel/bin:\ /apps1/pipe/bowtie/0.12.7/intel:\ /apps1/pipe/bwa/0.5.9/intel:\ /apps1/samtools/0.1.13/intel/bin:\ /apps1/fastx_toolkit/0.0.13/intel/bin:\ /apps1/maq/maq-0.7.1:\ /apps1/maq/maq-0.7.1/scripts:\ /apps1/bfast/bfast-0.6.5a/butil:\ /apps1/bfast/bfast-0.6.5a/scripts:\ /apps1/abyss/1.2.7/intel/bin:\ /apps1/velvet/velvet_1.0.12:\ /apps1/pipe/tophat/1.3.0/intel/bin:\ /apps1/pipe/cufflinks/1.0.3/intel/bin:\ /apps1/blast/2.2.25/gnu/bin:\ /apps1/blast+/2.2.5/gnu/bin:\ /apps1/sputnik/intel/bin:\ /apps1/taxonomy/intel/bin:\ /apps1/add_scores/add_scores:\ /apps1/emboss/6.4.0/intel/bin:\ /apps1/hyphy/hyphy/HYPHY:\ /apps1/lastz/1.02.00:\ /apps1/perm/0.3.6/intel/bin:\ /apps1/beam2/intel/bin:\ /apps1/pass2/intel/bin:\ /apps1/plink/1.07/intel/bin:\ /apps1/fbat/2.0.3/bin:\ /apps1/eigensoft/3.0/intel/bin:\ /apps1/mosaik/Mosaik-1.1.0021-Linux-x64/bin:\ /apps1/freebayes/freebayes.git/bin:\ $PATH export LD_LIBRARY_PATH=.:\ /apps1/python/2.6.6/intel/lib:\ /apps1/libgtextutils/0.6/intel/lib:\ /apps1/emboss/6.4.0/intel/lib:\ /apps1/intel/lib/intel64:\ /apps1/intel/mkl/lib/em64t:\ /apps1/tcltk/8.5.9/intel/lib:\ /apps1/zlib/1.2.5/intel/lib:\ /apps1/graphviz/2.26.3/intel/lib:\ /apps1/python/2.6.6/intel/lib/python2.6/site-packages/simtk/chem/openmm/OpenMM:\ /apps1/python/2.6.6/intel/lib/python2.6/site-packages:\ /apps1/libpng/1.5.0/intel/lib:\ /apps1/R/2.13.1/intel/lib64/R/lib:\ $LD_LIBRARY_PATH export PKG_CONFIG_PATH=.:\ /apps1/R/2.13.1/intel/lib64/pkgconfig:\ /apps1/libgtextutils/0.6/intel/lib/pkgconfig:\ /apps1/sparsehash/1.11/intel/lib/pkgconfig:\ $PKG_CONFIG_PATH export CLASSPATH=.:\ /apps1/gatk/gatk-git/dist:\ /apps1/gatk/gatk-git/lib:\ /apps1/srma/srma-0.1.13:\ /apps1/haploview/4.2:\ /apps1/picard/picard-tools-1.50:\ /apps1/fastqc/fastqc-0.9.5:\ $CLASSPATH best, joe ___ 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] [galaxy-user] mi-tools- tools_fabfile.py permissions requirements (local install)
R - not the correct download url, Which URL are you talking about? The wiki page on dependencies http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies correctly links to the R project as http://www.r-project.org/ you are correct, however the tools_fabfile.py has version = 2.11.1 url = http://mira.sunsite.utk.edu/CRAN/src/base/R-2/R-%s.tar.gz; % version rpy - will this be fixed? What needs to be fixed? Moving Galaxy to rpy2? https://bitbucket.org/galaxy/galaxy-central/issue/103/upgrade-rpy-to-latest-version again script has a comment: def _install_rpy(): # *Does not work in reality* Do you mean installing Galaxy without admin rights (i.e. without using sudo)? either way - but should work. The fab script for instance adds some jar files to the galaxy-dist structure - then more added via the same script as sudo, and when it wants to change permissions for the entire folder for the next application the script fails. Hence just curious what a smoother solution would be. In general - is the cloud install using the mi- script to install the tools? If so, where is it located? I'd like to compare it to the one i use for the local install. If it uses another script where/what is it? thanks, joe ___ 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] [galaxy-user] mi-tools- tools_fabfile.py permissions requirements (local install)
Hi, so for local install i can uncomment the R and rpy from your script as far as at the _install_R.. part? j From: Enis Afgan [eaf...@emory.edu] Sent: Monday, August 01, 2011 12:37 PM To: Joseph Hargitai Cc: Galaxy Dev Subject: Re: [galaxy-user] mi-tools- tools_fabfile.py permissions requirements (local install) Hi Joe, mi-deployment scripts are currently being used to create cloud images so this is the correct code your looking at. However, when it comes to R and rpy, those tools are (as you discovered) not being installed via those scripts; they are installed from packages but, in the case of Galaxy cloud images, they are inherited from the CloudBioLinux images that the Galaxy cloud images build on top of so not even included in the mi-deployment scripts. If you would like to follow suit and install those tools from packages, these are the ones (for debian): r-base, r-base-core, r-base-core-ra, r-base-dev, r-base-html, python-rpy As far as the permissions issues goes, I'll look (over the next couple of days) more closely at those and focus on consistency. Enis On Mon, Aug 1, 2011 at 11:04 AM, Peter Cock p.j.a.c...@googlemail.commailto:p.j.a.c...@googlemail.com wrote: Hi Jeseph, I see now you are talking about Enis' code for automated building of virtual machine Galaxy images, https://bitbucket.org/afgane/mi-deployment/src - mentioned briefly here: http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup I know very little about this area of Galaxy - we install any tools needed for Galaxy by hand (and try to document how we did it for future reference). On Mon, Aug 1, 2011 at 3:50 PM, Joseph Hargitai joseph.hargi...@einstein.yu.edumailto:joseph.hargi...@einstein.yu.edu wrote: R - not the correct download url, Which URL are you talking about? The wiki page on dependencies http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies correctly links to the R project as http://www.r-project.org/ you are correct, however the tools_fabfile.py has version = 2.11.1 url = http://mira.sunsite.utk.edu/CRAN/src/base/R-2/R-%s.tar.gz; % version That was a CRAN mirror, which seems to have gone now. Not listed here: http://cran.r-project.org/mirrors.html rpy - will this be fixed? What needs to be fixed? Moving Galaxy to rpy2? https://bitbucket.org/galaxy/galaxy-central/issue/103/upgrade-rpy-to-latest-version again script has a comment: def _install_rpy(): # *Does not work in reality* Do you mean installing Galaxy without admin rights (i.e. without using sudo)? either way - but should work. The fab script for instance adds some jar files to the galaxy-dist structure - then more added via the same script as sudo, and when it wants to change permissions for the entire folder for the next application the script fails. Hence just curious what a smoother solution would be. In general - is the cloud install using the mi- script to install the tools? If so, where is it located? I'd like to compare it to the one i use for the local install. If it uses another script where/what is it? thanks, joe Regards, 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: http://lists.bx.psu.edu/
