[galaxy-dev] Galaxy crach while visualization
Hello Galaxy team ! I have e strange problem whith my Galaxy trackster visualization . While viewing bookmarked regions in my visualisation the whole Galaxy process crashed and needed to be restarted, mainly when I use Chrome browser. Above the Paster.log : xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] GET /galaxy/tracks/data?chrom=chr19low=1183972high=1185154mode=Autoresolution=2.954022988505747dataset_id=f4b17be90d9b3c9dhda_ldda=hdafilter_cols=%5B%22Score%22%5D HTTP/1.1 200 - http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11 xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] GET /galaxy/tracks/data?chrom=chr19low=1182790high=1183972mode=Autoresolution=2.954022988505747dataset_id=ec90add676cb0ccehda_ldda=hdafilter_cols=%5B%22Mapping+Quality%22%5D HTTP/1.1 200 - http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11 xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] GET /galaxy/tracks/data?chrom=chr19low=1181609high=1182791mode=Autoresolution=2.954022988505747dataset_id=ec90add676cb0ccehda_ldda=hdafilter_cols=%5B%22Mapping+Quality%22%5D HTTP/1.1 200 - http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11 xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] GET /galaxy/tracks/data?chrom=chr19low=1183972high=1185154mode=Autoresolution=2.954022988505747dataset_id=ec90add676cb0ccehda_ldda=hdafilter_cols=%5B%22Mapping+Quality%22%5D HTTP/1.1 200 - http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11 xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] GET /galaxy/tracks/data?chrom=chr19low=1180427high=1181609mode=Autoresolution=2.954022988505747dataset_id=cc26e7b927e75a3dhda_ldda=hdafilter_cols=%5B%22Score%22%5D HTTP/1.1 200 - http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11 xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] GET /galaxy/tracks/data?chrom=chr19low=1181609high=1182791mode=Autoresolution=2.954022988505747dataset_id=cc26e7b927e75a3dhda_ldda=hdafilter_cols=%5B%22Score%22%5D HTTP/1.1 200 - http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11 xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] GET /galaxy/tracks/data?chrom=chr19low=1182790high=1183972mode=Autoresolution=2.954022988505747dataset_id=cc26e7b927e75a3dhda_ldda=hdafilter_cols=%5B%22Score%22%5D HTTP/1.1 200 - http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11 xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:37 +0200] GET /galaxy/tracks/data?chrom=chr19low=814128high=815310mode=Autoresolution=2.954022988505747dataset_id=7710e7c5028b7c3bhda_ldda=hdafilter_cols=%5B%22Score%22%5D HTTP/1.1 200 - http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11 PostgreSQL saw the crach : 2012-07-12 12:56:40 CEST LOG: could not receive data from client: Connection reset by peer 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:00:46.907 user=user database=database host=server port=33106 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:03:45.206 user=user database=database host=server port=42867 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:06:43.257 user=user database=database host=server port=56383 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:04:22.120 user=user database=database host=server port=42663 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:04:22.596 user=user database=database host=server port=42656 Thanks Amine ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other
Re: [galaxy-dev] cannot fetch egg svgfig from http://eggs.g2.bx.psu.edu
This is still not working. is it just me ? galaxdev@galaxy1:~$ hg clone https://bitbucket.org/galaxy/galaxy-dist galaxy-dist3 requesting all changes adding changesets adding manifests adding file changes added 7149 changesets with 28071 changes to 5807 files updating to branch default 3772 files updated, 0 files merged, 0 files removed, 0 files unresolved galaxdev@galaxy1:~$ cd galaxy-dist3 galaxdev@galaxy1:~/galaxy-dist3$ galaxy-slurm-setup slurm config written to universe_wsgi.ini drmaa config written to eggs.ini This is a new install. Do you also want to configure this instance for production? [Y/N]: n galaxdev@galaxy1:~/galaxy-dist3$ galaxdev@galaxy1:~/galaxy-dist3$ sh ./run.sh Initializing community_wsgi.ini from community_wsgi.ini.sample Initializing datatypes_conf.xml from datatypes_conf.xml.sample Initializing external_service_types_conf.xml from external_service_types_conf.xml.sample Initializing migrated_tools_conf.xml from migrated_tools_conf.xml.sample Initializing reports_wsgi.ini from reports_wsgi.ini.sample Initializing shed_tool_conf.xml from shed_tool_conf.xml.sample Initializing tool_conf.xml from tool_conf.xml.sample Initializing tool_data_table_conf.xml from tool_data_table_conf.xml.sample Initializing tool_sheds_conf.xml from tool_sheds_conf.xml.sample Initializing openid_conf.xml from openid_conf.xml.sample Initializing tool-data/shared/ucsc/builds.txt from builds.txt.sample Initializing tool-data/shared/igv/igv_build_sites.txt from igv_build_sites.txt.sample Initializing tool-data/shared/rviewer/rviewer_build_sites.txt from rviewer_build_sites.txt.sample Initializing tool-data/add_scores.loc from add_scores.loc.sample Initializing tool-data/alignseq.loc from alignseq.loc.sample Initializing tool-data/all_fasta.loc from all_fasta.loc.sample Initializing tool-data/annotation_profiler_options.xml from annotation_profiler_options.xml.sample Initializing tool-data/annotation_profiler_valid_builds.txt from annotation_profiler_valid_builds.txt.sample Initializing tool-data/bfast_indexes.loc from bfast_indexes.loc.sample Initializing tool-data/binned_scores.loc from binned_scores.loc.sample Initializing tool-data/blastdb.loc from blastdb.loc.sample Initializing tool-data/blastdb_p.loc from blastdb_p.loc.sample Initializing tool-data/bowtie2_indices.loc from bowtie2_indices.loc.sample Initializing tool-data/bowtie_indices.loc from bowtie_indices.loc.sample Initializing tool-data/bowtie_indices_color.loc from bowtie_indices_color.loc.sample Initializing tool-data/bwa_index.loc from bwa_index.loc.sample Initializing tool-data/bwa_index_color.loc from bwa_index_color.loc.sample Initializing tool-data/ccat_configurations.loc from ccat_configurations.loc.sample Initializing tool-data/codingSnps.loc from codingSnps.loc.sample Initializing tool-data/encode_datasets.loc from encode_datasets.loc.sample Initializing tool-data/faseq.loc from faseq.loc.sample Initializing tool-data/funDo.loc from funDo.loc.sample Initializing tool-data/gatk_annotations.txt from gatk_annotations.txt.sample Initializing tool-data/gatk_sorted_picard_index.loc from gatk_sorted_picard_index.loc.sample Initializing tool-data/lastz_seqs.loc from lastz_seqs.loc.sample Initializing tool-data/liftOver.loc from liftOver.loc.sample Initializing tool-data/maf_index.loc from maf_index.loc.sample Initializing tool-data/maf_pairwise.loc from maf_pairwise.loc.sample Initializing tool-data/microbial_data.loc from microbial_data.loc.sample Initializing tool-data/mosaik_index.loc from mosaik_index.loc.sample Initializing tool-data/ngs_sim_fasta.loc from ngs_sim_fasta.loc.sample Initializing tool-data/perm_base_index.loc from perm_base_index.loc.sample Initializing tool-data/perm_color_index.loc from perm_color_index.loc.sample Initializing tool-data/phastOdds.loc from phastOdds.loc.sample Initializing tool-data/picard_index.loc from picard_index.loc.sample Initializing tool-data/quality_scores.loc from quality_scores.loc.sample Initializing tool-data/regions.loc from regions.loc.sample Initializing tool-data/sam_fa_indices.loc from sam_fa_indices.loc.sample Initializing tool-data/sequence_index_base.loc from sequence_index_base.loc.sample Initializing tool-data/sequence_index_color.loc from sequence_index_color.loc.sample Initializing tool-data/sift_db.loc from sift_db.loc.sample Initializing tool-data/srma_index.loc from srma_index.loc.sample Initializing tool-data/twobit.loc from twobit.loc.sample Initializing static/welcome.html from welcome.html.sample Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2.bx.psu.edu/pysam/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/sqlalchemy_migrate/sqlalchemy_migrate-0.5.4-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.7.egg Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.7.egg Fetched
[galaxy-dev] Set metadata from within the tool
Hi everyone,
How can I set dataset's metadata from within the tool?
For example: From the command tag (in the xml tool specification) i
call myscript.sh:
command
myscript.sh -input=$input -output=$output
/command
My script.sh produce a value that i want to store as metadata of $input.
I've checked the tool config syntax
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax and seems
that i can read metadata (${input.metadata.somemetadata}) but not write.
Maybe code tag can help me but it is deprecated.
Thanks for the help,
Roberto
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Re: [galaxy-dev] Galaxy crach while visualization
Hello Amine, The paster log looks normal, and Postgre log is standard given the crash. Was there anything out of the ordinary that you can spot in the paster log and/or Javascript log in your Web browser? Thanks, J. On Jul 17, 2012, at 6:53 AM, Chebbi Mohamed Amine wrote: Hello Galaxy team ! I have e strange problem whith my Galaxy trackster visualization . While viewing bookmarked regions in my visualisation the whole Galaxy process crashed and needed to be restarted, mainly when I use Chrome browser. Above the Paster.log : xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] GET /galaxy/tracks/data?chrom=chr19low=1183972high=1185154mode=Autoresolution=2.954022988505747dataset_id=f4b17be90d9b3c9dhda_ldda=hdafilter_cols=%5B%22Score%22%5D HTTP/1.1 200 - http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11 xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] GET /galaxy/tracks/data?chrom=chr19low=1182790high=1183972mode=Autoresolution=2.954022988505747dataset_id=ec90add676cb0ccehda_ldda=hdafilter_cols=%5B%22Mapping+Quality%22%5D HTTP/1.1 200 - http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11 xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] GET /galaxy/tracks/data?chrom=chr19low=1181609high=1182791mode=Autoresolution=2.954022988505747dataset_id=ec90add676cb0ccehda_ldda=hdafilter_cols=%5B%22Mapping+Quality%22%5D HTTP/1.1 200 - http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11 xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] GET /galaxy/tracks/data?chrom=chr19low=1183972high=1185154mode=Autoresolution=2.954022988505747dataset_id=ec90add676cb0ccehda_ldda=hdafilter_cols=%5B%22Mapping+Quality%22%5D HTTP/1.1 200 - http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11 xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] GET /galaxy/tracks/data?chrom=chr19low=1180427high=1181609mode=Autoresolution=2.954022988505747dataset_id=cc26e7b927e75a3dhda_ldda=hdafilter_cols=%5B%22Score%22%5D HTTP/1.1 200 - http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11 xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] GET /galaxy/tracks/data?chrom=chr19low=1181609high=1182791mode=Autoresolution=2.954022988505747dataset_id=cc26e7b927e75a3dhda_ldda=hdafilter_cols=%5B%22Score%22%5D HTTP/1.1 200 - http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11 xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:36 +0200] GET /galaxy/tracks/data?chrom=chr19low=1182790high=1183972mode=Autoresolution=2.954022988505747dataset_id=cc26e7b927e75a3dhda_ldda=hdafilter_cols=%5B%22Score%22%5D HTTP/1.1 200 - http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11 xxx.xxx.xx.xxx, xxx.xx.xx.x - - [12/Jul/2012:12:56:37 +0200] GET /galaxy/tracks/data?chrom=chr19low=814128high=815310mode=Autoresolution=2.954022988505747dataset_id=7710e7c5028b7c3bhda_ldda=hdafilter_cols=%5B%22Score%22%5D HTTP/1.1 200 - http://xxx.xxx.com/galaxy/u/amine/v/rna-seq-analysis-tophats-output; Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_4) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.47 Safari/536.11 PostgreSQL saw the crach : 2012-07-12 12:56:40 CEST LOG: could not receive data from client: Connection reset by peer 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:00:46.907 user=user database=database host=server port=33106 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection 2012-07-12 12:56:40 CEST LOG: unexpected EOF on client connection 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:03:45.206 user=user database=database host=server port=42867 2012-07-12 12:56:40 CEST LOG: disconnection: session time: 0:06:43.257 user=user database=database host=server port=56383 2012-07-12 12:56:40 CEST LOG: disconnection:
[galaxy-dev] xsendfile permissions
Hi all, I'm wondering if someone who has downloads working through apache (using xsendfile) has encountered this error when downloading HTML files: (13)Permission denied: xsendfile: cannot open file: /galaxy_data/production/tmp/tmpN0ydYt/library_download.zip The output from ls -lZ /galaxy_data/production/tmp is: ... drwx--. galaxy galaxy unconfined_u:object_r:httpd_sys_content_t:s0 tmpN0ydYt ... The output from ls-lZ /galaxy_data/production/tmp/tmpN0ydYt/ is: -rw-rw-r--. galaxy galaxy unconfined_u:object_r:httpd_sys_content_t:s0 library_download.zip It's not a SElinux issue (if I sudo setenforce 0, the problem persists).. It seems it's a regular permissions issue (user apache is running httpd and does not permission to enter the tmpN0ydYt). Since galaxy creates these files with these permissions I don't know how to fix this issue. I'm also wondering why the HTML datasets are in the tmp folder not the files folder? Here's my apache config: VirtualHost *:80 ServerName RewriteEngine on #RewriteOptions Inherit #RewriteLog /etc/httpd/logs/rewrite_log #RewriteLogLevel 5 RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /usr/local/galaxy/production/galaxy-dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/scripts/(.*) /usr/local/galaxy/production/galaxy-dist/static/scripts/packed/$1 [L] RewriteRule ^/galaxy/static/(.*) /usr/local/galaxy/production/galaxy-dist/static/$1 [L] RewriteRule ^/galaxy/favicon.ico /usr/local/galaxy/production/galaxy-dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /usr/local/galaxy/production/galaxy-dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P] Location /galaxy order allow,deny allow from all # Compress all uncompressed content SetOutputFilter DEFLATE SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary # Send files through Apache XSendFile on XSendFilePath /galaxy_data /Location Location /galaxy/static # Allow browsers to cache everything from /static for 6 hours ExpiresActive On ExpiresDefault access plus 6 hours /Location /VirtualHost Is there something wrong with it? Or have I missed something in universe.wsgi? Cheers, Julian ___ 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] NTLM auth not passing http_remote_user?
It appears that NTLM isn't passing the HTTP_REMOTE_USER through for us.
Anyone else struck this and found a solution?
Our apache config looks like this:
Location /
AuthName Galaxy
NTLMAuth on
NTLMAuthHelper /usr/bin/ntlm_auth --helper-protocol=squid-2.5-ntlmssp
NTLMBasicAuthoritative on
AuthType NTLM
require valid-user
# Take the $REMOTE_USER environment variable and set it as a header in the
proxy request.
RewriteCond %{IS_SUBREQ} ^false$
RewriteCond %{LA-U:REMOTE_USER} (.+)
RewriteRule . - [E=RU:%1]
RequestHeader set REMOTE_USER %{RU}e
/Location
thanx,
--Russell
CONTENT_LENGTH
'0'
HTTP_ACCEPT
'*/*'
HTTP_ACCEPT_ENCODING
'gzip, deflate'
HTTP_ACCEPT_LANGUAGE
'en-NZ'
HTTP_AUTHORIZATION
'NTLM bla bla bla'
HTTP_CONNECTION
'Keep-Alive'
HTTP_COOKIE
'__utmc=89232139;
__utma=89232139.1132753487.1341174446.1342136886.1342560287.3;
__utmz=89232139.1342560287.3.3.utmcsr=gw.agresearch.co.nz|utmccn=(referral)|utmcmd=referral|utmcct=/Pages/Default.aspx;
__utmb=89232139.4.10.1342560287; galaxysession=c6ca0dd bla bla bla' bla bla
bla' bla bla bla' bla bla bla' bla bla bla' bla bla bla' bla bla bla' bla bla
bla' bla bla bla'
HTTP_HOST
'galaxy-dev.agresearch.co.nz'
HTTP_REMOTE_USER
'(null)'
HTTP_USER_AGENT
'Mozilla/4.0 (compatible; MSIE 7.0; Windows NT 6.1; WOW64; Trident/5.0; SLCC2;
.NET CLR 2.0.50727; .NET CLR 3.5.30729; .NET CLR 3.0.30729; Media Center PC
6.0; .NET CLR 1.1.4322; .NET4.0C; .NET4.0E; InfoPath.3)'
HTTP_X_FORWARDED_FOR
'147.158.129.160'
HTTP_X_FORWARDED_HOST
'galaxy-dev.agresearch.co.nz'
HTTP_X_FORWARDED_SERVER
'galaxy.agresearch.co.nz'
ORGINAL_HTTP_HOST
'localhost:8080'
ORGINAL_REMOTE_ADDR
'127.0.0.1'
PATH_INFO
'/'
REMOTE_ADDR
'147.158.129.160'
REQUEST_METHOD
'GET'
SERVER_NAME
'127.0.0.1'
SERVER_PORT
'8080'
SERVER_PROTOCOL
'HTTP/1.1'
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Re: [galaxy-dev] NTLM auth not passing http_remote_user?
Hello Russell,
Smithies, Russell wrote, On 07/17/2012 05:41 PM:
It appears that NTLM isn't passing the HTTP_REMOTE_USER through for us.
Anyone else struck this and found a solution?
Our apache config looks like this:
Location /
AuthName Galaxy
NTLMAuth on
NTLMAuthHelper /usr/bin/ntlm_auth --helper-protocol=squid-2.5-ntlmssp
NTLMBasicAuthoritative on
AuthType NTLM
require valid-user
# Take the $REMOTE_USER environment variable and set it as a header in
the proxy request.
RewriteCond %{IS_SUBREQ} ^false$
RewriteCond %{LA-U:REMOTE_USER} (.+)
RewriteRule . - [E=RU:%1]
RequestHeader set REMOTE_USER %{RU}e
/Location
snip
HTTP_REMOTE_USER
'(null)'
One voodoo solution that worked for me (not with NTLM, but exactly with the
same '(null)' symptom)
is to take the entire RewriteCond part outside of the Location block.
Put it in the global configuration file, after the Location part, but before
the proxy statement.
Also, the exact incantation that worked for me (after many many trials and
errors) is:
===
RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}]
RequestHeader set REMOTE_USER %{RU}e
===
It's voodoo (to me) because it probably has something to do with deep apache
internals, relating to execution order of the authentication module vs the
mod_rewrite parts (and the LA-U [Look-ahead] thing sure doesn't help to
make it clearer...).
-gordon
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[galaxy-dev] Attempting to use parallelism in BWA
To give this question better visibility, I am going to move it over to the galaxy-...@bx.psu.edu mailing list. Thanks! Jen Galaxy team fwd from galaxy-user On 7/17/12 11:31 AM, Scott McManus wrote: Hi Kevin- That's truly odd. The error happens when the offending file is imported, which means that it is a syntax issue that should have been seen earlier. I'll take a look at this soon (unless someone else beats me to it). In the meantime, of course, do not use the use_tasked_jobs on this instance of Galaxy. If others have seen similar issues, then please speak up. -Scott Hi, I am using Python 2.7. I am running with an hg checked out, up to date version of https://bitbucket.org/galaxy/galaxy-dist/;. I am very new to Galaxy. I have an instance setup *and running* locally. I am able to perform routine actions such as uploading files, processing with Picard, and aligning with BWA. I have been able to make the jobs execute out our SGE cluster. In order to better utilize my cluster, I attempted to enable parallelism of the tasks that support it (such as BWA) by configuring the *universe_wsgi.ini* file with the parameter use_tasked_jobs = True When I do this and attempt execute a BWA alignment on a 4.1Gb fastq file, I am given the error Result 256 from mv /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/job_working_directory/000/21/task_1/dataset_21.dat /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/files/000/dataset_21.dat /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/database/job_working_directory/000/21/task_0: Traceback (most recent call last): File ./scripts/extract_dataset_part.py, line 25, in ? import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers File /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/lib/galaxy/model/__init__.py, line 13, in ? import galaxy.datatypes.registry File /pbtech_mounts/fclab_store006/gobyweb_dat/galaxy-python/lib/galaxy/datatypes/registry.py, line 146 finally: ^ SyntaxError: invalid syntax The alignment failed. If you need the complete error message, contact me and I can supply you with it. It's too large to paste in-line and attachments aren't allowed. Is there more I need to do to enable parallel jobs (splitting of input, align, then merge)? Any suggestions are greatly appreciated. Kevin ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://galaxyproject.org ___ 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] NTLM auth not passing http_remote_user?
If I take the rewrite out of the location block then NTLM auth fails as the
username is re-written and isn't a valid corporate username.
On the plus side, If I just set RequestHeader set REMOTE_USER smithiesr then
I get logged in as I should.
--Russell
-Original Message-
From: Assaf Gordon [mailto:gor...@cshl.edu]
Sent: Wednesday, 18 July 2012 9:59 a.m.
To: Smithies, Russell
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] NTLM auth not passing http_remote_user?
Hello Russell,
Smithies, Russell wrote, On 07/17/2012 05:41 PM:
It appears that NTLM isn't passing the HTTP_REMOTE_USER through for us.
Anyone else struck this and found a solution?
Our apache config looks like this:
Location /
AuthName Galaxy
NTLMAuth on
NTLMAuthHelper /usr/bin/ntlm_auth --helper-protocol=squid-2.5-ntlmssp
NTLMBasicAuthoritative on
AuthType NTLM
require valid-user
# Take the $REMOTE_USER environment variable and set it as a header in
the proxy request.
RewriteCond %{IS_SUBREQ} ^false$
RewriteCond %{LA-U:REMOTE_USER} (.+)
RewriteRule . - [E=RU:%1]
RequestHeader set REMOTE_USER %{RU}e
/Location
snip
HTTP_REMOTE_USER
'(null)'
One voodoo solution that worked for me (not with NTLM, but exactly with the
same '(null)' symptom) is to take the entire RewriteCond part outside of the
Location block.
Put it in the global configuration file, after the Location part, but before
the proxy statement.
Also, the exact incantation that worked for me (after many many trials and
errors) is:
===
RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}] RequestHeader set REMOTE_USER %{RU}e
===
It's voodoo (to me) because it probably has something to do with deep apache
internals, relating to execution order of the authentication module vs the
mod_rewrite parts (and the LA-U [Look-ahead] thing sure doesn't help to
make it clearer...).
-gordon
===
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
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Re: [galaxy-dev] NTLM auth not passing http_remote_user?
Working now :- )
I blame lack of coffee - I hadn't set RewriteEngine on before I re-wrote the
request header.
It appears it needs to be in the location section or your initial ntlm auth
wil fail.
Location /
AuthName Galaxy
NTLMAuth on
NTLMAuthHelper /usr/bin/ntlm_auth --helper-protocol=squid-2.5-ntlmssp
NTLMBasicAuthoritative on
AuthType NTLM
require valid-user
# Take the $REMOTE_USER environment variable, trim the realm and set it as
a header in the proxy request.
RewriteEngine on
RewriteCond %{IS_SUBREQ} ^false$
RewriteCond %{LA-U:REMOTE_USER} .+\\(.+)
RewriteRule . - [E=RU:%1]
RequestHeader set REMOTE_USER %{RU}e
/Location
--Russell
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Smithies, Russell
Sent: Wednesday, 18 July 2012 10:52 a.m.
To: Assaf Gordon
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] NTLM auth not passing http_remote_user?
If I take the rewrite out of the location block then NTLM auth fails as the
username is re-written and isn't a valid corporate username.
On the plus side, If I just set RequestHeader set REMOTE_USER smithiesr then
I get logged in as I should.
--Russell
-Original Message-
From: Assaf Gordon [mailto:gor...@cshl.edu]
Sent: Wednesday, 18 July 2012 9:59 a.m.
To: Smithies, Russell
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] NTLM auth not passing http_remote_user?
Hello Russell,
Smithies, Russell wrote, On 07/17/2012 05:41 PM:
It appears that NTLM isn't passing the HTTP_REMOTE_USER through for us.
Anyone else struck this and found a solution?
Our apache config looks like this:
Location /
AuthName Galaxy
NTLMAuth on
NTLMAuthHelper /usr/bin/ntlm_auth --helper-protocol=squid-2.5-ntlmssp
NTLMBasicAuthoritative on
AuthType NTLM
require valid-user
# Take the $REMOTE_USER environment variable and set it as a header in
the proxy request.
RewriteCond %{IS_SUBREQ} ^false$
RewriteCond %{LA-U:REMOTE_USER} (.+)
RewriteRule . - [E=RU:%1]
RequestHeader set REMOTE_USER %{RU}e
/Location
snip
HTTP_REMOTE_USER
'(null)'
One voodoo solution that worked for me (not with NTLM, but exactly with the
same '(null)' symptom) is to take the entire RewriteCond part outside of the
Location block.
Put it in the global configuration file, after the Location part, but before
the proxy statement.
Also, the exact incantation that worked for me (after many many trials and
errors) is:
===
RewriteRule . - [E=RU:%{LA-U:REMOTE_USER}] RequestHeader set REMOTE_USER %{RU}e
===
It's voodoo (to me) because it probably has something to do with deep apache
internals, relating to execution order of the authentication module vs the
mod_rewrite parts (and the LA-U [Look-ahead] thing sure doesn't help to
make it clearer...).
-gordon
===
Attention: The information contained in this message and/or attachments from
AgResearch Limited is intended only for the persons or entities to which it is
addressed and may contain confidential and/or privileged material. Any review,
retransmission, dissemination or other use of, or taking of any action in
reliance upon, this information by persons or entities other than the intended
recipients is prohibited by AgResearch Limited. If you have received this
message in error, please notify the sender immediately.
===
___
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/
