[galaxy-dev] Add a private genome in database/build , only visible for a specific user connected on a local instance.
Hello, I would like to know if it's possible to limit the access to a private reference genome, for a specific user, in database/build field ? In fact, I would like that the reference genome is visible/shown only for a specific user connected to your local Galaxy instance, and hidden for others users. Should I specify something in galaxy-dist/tool-data/shared/ucsc/builds.txt file ? Thanks in advance, Sarah Maman -- --*-- Sarah Maman INRA - GenPhySE - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*-- ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] IVG display error / local instance of Galaxy
Hello, I try to connect my local instance of Galaxy to IGV but I receive this error message : *server redirected too many times (20)* I can see the IGV link in my dataset and I can open IGV thought my local instance but my dataset is not found. Here is modifiactions of my local instance: * My httpd.conf file has the location match added : | LocationMatch ^/galaxy/display_application/[a-zA-Z0-9]+/igv.*| |RequestHeader set REMOTE_USER igv_disp...@toulouse.inra.fr| |Satisfy Any| |Order deny,allow| |Allow from all| |/LocationMatch| * IGV is setted up as a display application in my local instance: |display file=igv/bam.xml / |* I new RewriteRule is now added in my httpd.conf file : RewriteRule ^/galaxy/display_application/[a-zA-Z0-9]+/igv_bam/web_link_main/[a-zA-Z0-9]+/data/galaxy_[a-zA-Z0-9]+.bam /path/to/my/galaxy/database/files/$1 [L] | | Do you have any idea ? Could you please help me ? Thanks in advance, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*-- ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Error / import rpy module
Hello, Some Galaxy tools failed to import rpy module and displays the following message: Traceback (most recent call last): File /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/plotting/histogram.py, line 5, in module from rpy import * ImportError: No module named rpy For instance, the tool Regrouping (tools/stats/grouping.py) have been refactored in 2011 by Kanwei Li to use numpy instead of rpy. And this tool runs on my local instance of Galaxy. But I would like to be able use rpy module instead of refactor the others tools. Could you, please, help me to understand why the eggs ' import does not allow the use of rpy module? How to debug these tools? Thnaks in advance, Sarah -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*-- ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error / import rpy module
Thanks a lot for these explantions, I have downloded refactored tools (rpy2 is more suited to our R version). Unfortunatly, galaxy still do not import rpy2 .. Traceback (most recent call last): File /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/plotting/histogram.py, line 6, in module import rpy2.robjects as robjects ImportError: No module named rpy2.robjects Moreover our rpy2 module is avalaible and listed in our python. Maybe a problem with Python ? Thanks in advance, Sarah Hans-Rudolf Hotz a écrit : Hi Sarah you need to install the rpy module: http://rpy.sourceforge.net/rpy.html As a warning: we have been struggling to get rpy to work with newer versions of R. In or experience in only works with R version 2.9 and older. Thanks to a recent effort of our sysadmin, we can now use it with 2.15 - which is good, but not great, as our default version of R is now 3.0 Although we haven't started to us it, I recommend using rpy2: http://rpy.sourceforge.net/rpy2.html Most tools have been refactored by John Chilton see: http://dev.list.galaxyproject.org/rpy2-Core-Tools-td4659832.html Regards, Hans-Rudolf On 06/05/2013 10:19 AM, Sarah Maman wrote: Hello, Some Galaxy tools failed to import rpy module and displays the following message: Traceback (most recent call last): File /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/plotting/histogram.py, line 5, in module from rpy import * ImportError: No module named rpy For instance, the tool Regrouping (tools/stats/grouping.py) have been refactored in 2011 by Kanwei Li to use numpy instead of rpy. And this tool runs on my local instance of Galaxy. But I would like to be able use rpy module instead of refactor the others tools. Could you, please, help me to understand why the eggs ' import does not allow the use of rpy module? How to debug these tools? Thnaks in advance, Sarah -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*-- ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Run galaxy on a specific SGE queue
Thanks Nate, In fact, our ~/.sge_request set workq by default. So, we have changed this parameter in ~/.sge_request file in order to change the working queue. Thanks again for your help, Sarah Nate Coraor a écrit : On May 22, 2013, at 11:36 AM, Sarah Maman wrote: Hi everyone, Galaxy is set up on our cluster, and so far everything is working just fine. However, we'd like to change the submission queue from the default to a specific one. To do so, we tryed to set on the universe_wsgi.ini file the default_cluster_job_runner parameter as following: default_cluster_job_runner = drmaa://-q test.q -l mem=8G -l h_vmem=10G/ When doing so, an error occured telling us the job has been rejected because 2 queues were specified: the workq (default one) and the test.q. Should be the queue setting this way ? What are we doing wrong ? Hi Sarah, Without knowing what's going on in your environment I can't say for sure, but I would guess that something else is (~/.sge_request?) is also attempting to set the queue. Are you able to use `qsub -q test.q` on the command line as the same user that runs Galaxy? Thanks, --nate thanks for your help, Sarah Sarah Maman INRA - LGC - SIGENAE Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*-- ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Information for Galaxy Event Horizon
Dear all, Four days of training in genomics are occurring on our local instance of Galaxy (27-30 May). This training session takes place at INRA, Toulouse Auzeville, France, as part of a collaboration between Sigenae (http://www.sigenae.org/) and GenoToul bioinformatics platform (http://bioinfo.genotoul.fr/). This session is composed of four training days: * Galaxy first step * Reads alignment and SNP calling * RNAseq alignment and transcripts assemblies * sRNAseq Do you think it is possible to list our training session in your Galaxy Event Horizon? Sincerely, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*-- ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Run galaxy on a specific SGE queue
Hi everyone, Galaxy is set up on our cluster, and so far everything is working just fine. However, we'd like to change the submission queue from the default to a specific one. To do so, we tryed to set on the universe_wsgi.ini file the default_cluster_job_runner parameter as following: default_cluster_job_runner = drmaa://-q test.q -l mem=8G -l h_vmem=10G/ When doing so, an error occured telling us the job has been rejected because 2 queues were specified: the workq (default one) and the test.q. Should be the queue setting this way ? What are we doing wrong ? thanks for your help, Sarah -- Sarah Maman INRA - LGC - SIGENAE Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Step 3 of get Microbial Data install
Hello, I try to set Get Microbial Data in my local instance of Galaxy. So, as explain in /path/to//src/galaxy/galaxy-dist/scripts/microbes/README.txt , step 1 and 2 or OK, binary 'faToNib' is available on our cluster, but step 3 generate empty files : drwxr-xr-x 4 galaxy wbioinfo 100 18 avril 14:26 .. -rw-r--r-- 1 galaxy wbioinfo 203 18 avril 14:26 harvest.txt -rw-r--r-- 1 galaxy wbioinfo 69 18 avril 14:34 ncbi_to_ucsc.txt -rw-r--r-- 1 galaxy wbioinfo 0 19 avril 15:47 sequence.txt -rw-r--r-- 1 galaxy wbioinfo 0 19 avril 15:47 seq.loc drwxr-xr-x 2 galaxy wbioinfo 118 19 avril 15:47 . Could you please, hel me ? Thnaks in advance, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*-- ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tophat didn't run
Thanks Jennifer, Since I did have an error when I run tophat2 with, as reference, a fasta from my history, so I modified line 105 of tophat wrapper (bowtie2-build instead of bowtie-build in command line). Now Tophat for Illumina Find splice junctions using RNA-seq data runs without error. Thank you again for your help, Sarah Jennifer Jackson a écrit : Hi Sarah, On 4/11/13 8:02 AM, Sarah Maman wrote: Thnaks Jennifer, Excuse me, my previous mail contains an error : In fact, the reference genome from my history was a fasta format (the name was GTF file but the format was fasta...). So, when I run tophat with a reference genome from your history, here is the error message (my reference genome is a FASTA file) : OK, now this looks like a tool/index mismatch problem. Most likely rooted in a binary path issue. Error in tophat: [2013-04-11 14:57:12] Beginning TopHat run (v2.0.5) --- [2013-04-11 14:57:12] Checking for Bowtie Bowtie version:2.0.0.7 [2013-04-11 14:57:12] Checking for Samtools Samtools version:0.1.19.0 [2013-04-11 14:57:13] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/tmp/1078173.1.workq/tmpzxEFNK/dataset_6485.*.bt2) Settings: blablabla OK. Total time for backward call to driver() for mirror index: 00:00:57 TopHat v2.0.5 tophat -p 4 /tmp/1078173.1.workq/tmpzxEFNK/dataset_6485 /work/galaxy/database/files/006/dataset_6528.dat [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM file. Epilog : job finished at jeu. avril 11 14:57:18 CEST 2013 And here is my bowtie and tophat versions : $ which bowtie bowtie -v 0.12.8 This is good $ which tophat tophat -v 2.0.5 This is most likely the problem. There is probably a symbolic link pointing from tophat - tophat2. You will want to remove that. The tool wrappers will be looking for the correct binary/indexes for the version they are each dependent on. This means that if you are running Tophat2 for Illumina, you want both tophat2 and bowtie2 to be used, along with the bowtie2 indexes. This is detailed in the wikis I sent in the Tophat/Bowtie sections, for both dependencies and the index set up. My guess at this point, without seeing your exact files, is that you need to add the index path to the bowtie2 loc file, and remove/adjust the symbolic link as I stated above, then restart, and test again to see if that fixes the problem. But we have also, available on our cluster : bowtie2 --version is 2.0.0-beta7 This is also good, if which bowtie == v0.12.8 and which bowtie2 == v2. If bowtie is pointing to v2 on your cluster nodes, then remove that symbolic link, so that this is instead pointing to the correct binary (v0.12.8). same for bowtie2, should point to the v2 binary. bowtie/tophat and bowtie2/tophat2 are not the same executable and use different indexes - this is most likely why you had to use the bowtie v0.12.8 loc to get tophat2 going to begin with. Hope it works this time! Please keep replies on the list to help us with tracking, Jen Galaxy team Could you please tell me how to point to the v2 binaries (how to change symbolic links) ? Thanks in advance, Sarah Jennifer Jackson a écrit : Hi Sarah, It still sounds like there is a path problem - this is why the tools are looking in the wrong loc file. When bowtie2/tophat2 installs, it will create a symbolic link that names itself as just bowtie or tophat, pointing to the v2 binaries. When you run these, what do you get? $ which bowtie $ which tophat My guess is that these are symbolic links pointing to the v2 binaries. You will want to remove these. This is noted in the NGS set-up wiki, but easy to miss. For the custom _reference genome _portion below, there is a mix-up here. A custom _reference genome_ is in fasta format, not GTF format. I think what you are doing is using a _reference annotation_ file with the process. Both can be used with RNA-seq tools, but the _reference genome_ is the one with the indexes. The link I sent about _custom reference genomes_ explains how to use one of these, if you still what want to try. I think it is worth reviewing the path and loc info, plus the binary commands above. Unless this helps you to solve the problem on your own now. Thanks! Jen Galaxy team On 4/11/13 6:16 AM, Sarah Maman wrote: Thanks a lot Jennifer, Restart, full paths were OK. I don't know why but the 2nd version of Tophat (so the tophat tool available from Galaxy) search indexs in bowtie-index.loc file and not in bowtie2-index.loc So, I've added my bowtie2 index paths in bowtie-index. loc file and tophat run... But when I want to run tophat with a reference genome from your history, here
Re: [galaxy-dev] Tophat didn't run
Thanks a lot Jennifer, Restart, full paths were OK. I don't know why but the 2nd version of Tophat (so the tophat tool available from Galaxy) search indexs in bowtie-index.loc file and not in bowtie2-index.loc So, I've added my bowtie2 index paths in bowtie-index. loc file and tophat run... But when I want to run tophat with a reference genome from your history, here is the error message (my reference genome is a GFT file) : Error in tophat: [2013-04-11 14:57:12] Beginning TopHat run (v2.0.5) --- [2013-04-11 14:57:12] Checking for Bowtie Bowtie version:2.0.0.7 [2013-04-11 14:57:12] Checking for Samtools Samtools version:0.1.19.0 [2013-04-11 14:57:13] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/tmp/1078173.1.workq/tmpzxEFNK/dataset_6485.*.bt2) Settings: blablabla OK. Total time for backward call to driver() for mirror index: 00:00:57 TopHat v2.0.5 tophat -p 4 /tmp/1078173.1.workq/tmpzxEFNK/dataset_6485 /work/galaxy/database/files/006/dataset_6528.dat [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM file. Epilog : job finished at jeu. avril 11 14:57:18 CEST 2013 Thanks in advance, Sarah Jennifer Jackson a écrit : Hi Sarah, Let's try to sort this out. Your problem does not seem to be the same as in the question referenced, but we can see. First - just to double check - since setting up the genome, you have restarted the server? If not, do that first and check to see if that fixes the problem. Basically, you want to follow this checklist and restarting is the final step: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup If the problem persists, then would you please send a few more details: 1 - full paths* on you system where you keep the .bt2 indexes, sam index, and .fa file. Maybe do an ls -l on these dirs so we can check the symbolic links are in place and named correctly. * as a note, these should be hard paths and not symbolic (except for the .fa links), and must have permissions set to be accessible to the galaxy user 2 - lines from your bowtie2_indices.loc and sam_fa_indices.loc file for this genome. I may have you double check your builds.txt file later. if this doesn't sounds familiar, it could be the problem, the genome must be in there, too. - see this wiki: http://wiki.galaxyproject.org/Admin/Data%20Integration 3 - full error message you get when you try to run this using a genome in fasta format from your history. It really shouldn't be the same error - something is not right with the settings and a custom genome is not actually being used if that is the case. Give it another try and see what happens, then send that info. This is a bit of a side case, we should get your basic install correct, but knowing how to do this is a good thing and easy to learn. http://wiki.galaxyproject.org/Support#Custom_reference_genome It is OK to masked out anything like user names/groups you don't want to share. Please keep on the list in case we need other feedback. Thanks! Jen Galaxy team On 4/10/13 3:15 AM, Sarah Maman wrote: Hello, When I run tophat (Tophat for Illumina Find splice junctions using RNA-seq data ), the job failed with truncated files. However, index files are available and I get exactly the same error message using built-in index or one of my history. / Tool execution generated the following error message: Error in tophat: [2013-04-10 09:17:07] Beginning TopHat run (v2.0.5) --- [2013-04-10 09:17:07] Checking for Bowtie Bowtie version: 2.0.0.7 [2013-04-10 09:17:07] Checking for Samtools Samtools version: 0.1.19.0 [2013-04-10 09:17:07] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/work/galaxy/Danio_rerio.Zv9.62.dna.chromosome.22.fa.*.bt2) The tool produced the following additional output: TopHat v2.0.5 tophat -p 4 /work/galaxy/Danio_rerio.Zv9.62.dna.chromosome.22.fa /work/galaxy/database/files/006/dataset_6528.dat [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM file. Epilog : job finished at mer. avril 10 09:17:12 CEST 2013 / In this post (http://dev.list.galaxyproject.org/tophat-for-illumina-looking-in-wrong-directory-for-bowtie2-indexes-tt4658609.html#none), the solution isn't found. Do you have any idea, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53
[galaxy-dev] Tophat didn't run
Hello, When I run tophat (Tophat for Illumina Find splice junctions using RNA-seq data ), the job failed with truncated files. However, index files are available and I get exactly the same error message using built-in index or one of my history. / Tool execution generated the following error message: Error in tophat: [2013-04-10 09:17:07] Beginning TopHat run (v2.0.5) --- [2013-04-10 09:17:07] Checking for Bowtie Bowtie version: 2.0.0.7 [2013-04-10 09:17:07] Checking for Samtools Samtools version: 0.1.19.0 [2013-04-10 09:17:07] Checking for Bowtie index files Error: Could not find Bowtie 2 index files (/work/galaxy/Danio_rerio.Zv9.62.dna.chromosome.22.fa.*.bt2) The tool produced the following additional output: TopHat v2.0.5 tophat -p 4 /work/galaxy/Danio_rerio.Zv9.62.dna.chromosome.22.fa /work/galaxy/database/files/006/dataset_6528.dat [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [bam_index_core] Invalid BAM header.[bam_index_build2] fail to index the BAM file. Epilog : job finished at mer. avril 10 09:17:12 CEST 2013 / In this post (http://dev.list.galaxyproject.org/tophat-for-illumina-looking-in-wrong-directory-for-bowtie2-indexes-tt4658609.html#none), the solution isn't found. Do you have any idea, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*-- ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] hg pull aborted
Hello, When updating local instance of our Galaxy, the hg aborted: pulling from https://bitbucket.org/galaxy/galaxy-dist/ searching for changes adding changesets adding manifests adding file changes added 1482 changesets with 3989 changes to 1340 files abort: untracked file in working directory differs from file in requested revision: 'doc/Makefile' and : -bash-3.2$ hg update abort: untracked file in working directory differs from file in requested revision: 'doc/source/conf.py' Could you please tell me what this may be the problem? Thanks ___ 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] Server Error / Edit attribut of a dataset generated by a tool
Hi Daniel, In fact, my version needs to be updated : changeset: 6799:40f1816d6857 tag: tip user:Greg Von Kuster g...@bx.psu.edu date:Wed Mar 07 13:35:34 2012 -0500 summary: Fix for populating the tool panel and generating the integrated_tool_panel.xml file. I try and let you know. Sarah Daniel Blankenberg d...@bx.psu.edu a écrit : Hi Sarah, This looks to be due to a non-unicode character in the dataset's info field. Are you using a Galaxy revision = 7563:fca4e12478d6? Thanks for using Galaxy, Dan On Dec 11, 2012, at 8:25 AM, Sarah Maman wrote: Hello, One of my users gets the following message when he wishes to edit the attribute of a dataset which is generated by using a tool (same problem as it is a tool provided by Galaxy or a tool coded by us). Do you have any idea? Thanks in advance, Sarah Maman URL: http://sigenae-workbench.toulouse.inra.fr/galaxy/datasets/b9580783e2098a2b/edit File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 111 in __call__ return self.app( environ, start_response ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/controllers/dataset.py', line 600 in edit refresh_frames=refresh_frames ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 722 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 733 in fill_template_mako return template.render( **data ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/base.mako.py', line 42 in render_body __M_writer(unicode(next.body())) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/dataset/edit_attributes.mako.py', line 95 in render_body __M_writer(filters.html_escape(unicode(data.info ))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 31: ordinal not in range(128) ___ 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/ -- Sarah Maman INRA - LGC - SIGENAE Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 ___ 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] Server Error / Edit attribut of a dataset generated by a tool
Hello, One of my users gets the following message when he wishes to edit the attribute of a dataset which is generated by using a tool (same problem as it is a tool provided by Galaxy or a tool coded by us). Do you have any idea? Thanks in advance, Sarah Maman URL: http://sigenae-workbench.toulouse.inra.fr/galaxy/datasets/b9580783e2098a2b/edit File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py', line 111 in __call__ return self.app( environ, start_response ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/controllers/dataset.py', line 600 in edit refresh_frames=refresh_frames ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 722 in fill_template return self.fill_template_mako( filename, **kwargs ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 733 in fill_template_mako return template.render( **data ) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/template.py', line 296 in render return runtime._render(self, self.callable_, args, data) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 660 in _render **_kwargs_for_callable(callable_, data)) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 692 in _render_context _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/Mako-0.4.1-py2.6.egg/mako/runtime.py', line 718 in _exec_template callable_(context, *args, **kwargs) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/base.mako.py', line 42 in render_body __M_writer(unicode(next.body())) File '/usr/local/bioinfo/src/galaxy/galaxy-dist/database/compiled_templates/dataset/edit_attributes.mako.py', line 95 in render_body __M_writer(filters.html_escape(unicode(data.info ))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 31: ordinal not in range(128) ___ 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] Impossible to add a (new) tool in a workflow (in edition mode)
Hello, For one of my tools that I have added to my local instance of Galaxy, I can not add this tool in the editing workflow. When I click on the tool name in the tools windows on the left, it does not appear in the editing workflow. Do you have any idea? Thank you in advance, Sarah Maman ___ 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] Impossible to add a (new) tool in a workflow (in edition mode)
Thanks Danon, But I have no error generated in my error log file (logs of run.sh): [11/Dec/2012:16:39:09 +0200] GET /galaxy/workflow HTTP/1.1 200 - http://URL/galaxy/root; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:11 +0200] GET /galaxy/workflow/editor?id=7085c9c37b8829fc HTTP/1.1 200 - http://URL/galaxy/workflow; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:12 +0200] GET /galaxy/workflow/get_datatypes?_=1355240375711 HTTP/1.1 200 - http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:12 +0200] GET /galaxy/workflow/load_workflow?id=7085c9c37b8829fc_=1355240375756 HTTP/1.1 200 - http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:17 +0200] GET /galaxy/workflow/get_new_module_info?type=tooltool_id=BWA_miRNA_=true HTTP/1.1 200 - http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 Others actions are listed by not my click on this tool's name. Is paster.log file a default file of Galaxy? Where could I find this file ? Sarah Dannon Baker a écrit : Do you see any errors in Galaxy's paster.log, or in the javascript console? -Dannon On Dec 11, 2012, at 8:40 AM, Sarah Maman sarah.ma...@toulouse.inra.fr wrote: Hello, For one of my tools that I have added to my local instance of Galaxy, I can not add this tool in the editing workflow. When I click on the tool name in the tools windows on the left, it does not appear in the editing workflow. Do you have any idea? Thank you in advance, Sarah Maman ___ 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] Impossible to add a (new) tool in a workflow (in edition mode)
Dannon, Here is myjavascript console errors : SyntaxError: missing ) after argument list : /* ool( 'sm_miRNA_join_annot', '* Construction de la matrice d'annotations' ) */ /*editor...8829fc# (ligne 1, col. 60)*/ I replaced this syntax Construction de la matrice d'annotations by the latter Construction de la matrice d annotations, and thank you, now it works! Thanks a lot, Sarah Dannon Baker a écrit : The paster.log is just the file for the output you've copied below when running daemonized -- if you're running in the foreground it just gets sent there instead of to the file. So, no obvious errors there. Could you check for javascript console errors? And, if you'd like, feel free to send the tool xml to me directly and I'll try to see if I can reproduce the issue. -Dannon On Dec 11, 2012, at 10:47 AM, Sarah Maman sarah.ma...@toulouse.inra.fr wrote: Thanks Danon, But I have no error generated in my error log file (logs of run.sh): [11/Dec/2012:16:39:09 +0200] GET /galaxy/workflow HTTP/1.1 200 - http://URL/galaxy/root; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:11 +0200] GET /galaxy/workflow/editor?id=7085c9c37b8829fc HTTP/1.1 200 - http://URL/galaxy/workflow; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:12 +0200] GET /galaxy/workflow/get_datatypes?_=1355240375711 HTTP/1.1 200 - http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:12 +0200] GET /galaxy/workflow/load_workflow?id=7085c9c37b8829fc_=1355240375756 HTTP/1.1 200 - http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 IP - - [11/Dec/2012:16:39:17 +0200] GET /galaxy/workflow/get_new_module_info?type=tooltool_id=BWA_miRNA_=true HTTP/1.1 200 - http://URL/galaxy/workflow/editor?id=7085c9c37b8829fc; Mozilla/5.0 (Windows NT 6.1; WOW64; rv:17.0) Gecko/20100101 Firefox/17.0 Others actions are listed by not my click on this tool's name. Is paster.log file a default file of Galaxy? Where could I find this file ? Sarah Dannon Baker a écrit : Do you see any errors in Galaxy's paster.log, or in the javascript console? -Dannon On Dec 11, 2012, at 8:40 AM, Sarah Maman sarah.ma...@toulouse.inra.fr wrote: Hello, For one of my tools that I have added to my local instance of Galaxy, I can not add this tool in the editing workflow. When I click on the tool name in the tools windows on the left, it does not appear in the editing workflow. Do you have any idea? Thank you in advance, Sarah Maman ___ 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] How to modify save icon
Hello, The tool SAM to BAM generates a dataset from which it is possible to download two files (instead of one) from the icon save. As my script generates an output result and another txt output containing information about linux command, I will wish not to generate two datasets in history but only one dataset with two files downloaded from the icon save. Do you know how to encode the corresponding xml? Moreover, I would like to add file formats of file which can be opened in the central window central of Galaxy (thanks to eye icon). Do you know, please, how to add more files formats ? Thanks in advance, Sarah Mom ___ 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] GFF tools
Hello, When I use one of GFF tool ( Filter GFF data by attribute http://sig-workbench.toulouse.inra.fr/galaxy/tool_runner?tool_id=gff_filter_by_attribute using simple expressions OR Filter GFF data by feature count http://sig-workbench.toulouse.inra.fr/galaxy/tool_runner?tool_id=gff_filter_by_feature_count using simple expressions OR Filter GTF data by attribute values_list http://sig-workbench.toulouse.inra.fr/galaxy/tool_runner?tool_id=gtf_filter_by_attribute_values_list) , I have this message : Traceback (most recent call last): File /usr/local/bioinfo/src/galaxy/galaxy-dist/tools/filters/gff/gff_filter_by_attribute.py, line 55, in module attribute_types = from_json_string( sys.argv[4] ) File /usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/__init__.py, line 384, in loads File /usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py, line 402, in decode File /usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg/simplejson/decoder.py, line 420, in raw_decode simplejson.decoder.JSONDecodeError: No JSON object could be decoded: line 1 column 0 (char 0) Could you please help me ? Thanks in advance, Sarah Maman ___ 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] Tool added / pb with output file
Hello,
My problem is solved. Here is a solution :
my $output_galaxy = $ARGV[2];
.
if (! -e $output_perl_file) {print STDERR no output file\n;}
else {`(cp -a $output_perl_file $output_galaxy) ./error.log 21`}
And an explanation :
The output file generated by commands in my perl script is not the same
file that the output file generated by Galaxy. So, I have to copy or
move the content of the output file generated by my perl script in the
Galaxy output file (arg).
I'll will add my tool in Galaxy Tool Shed (perl script have been modified).
Faithfully,
Sarah Maman
Sarah Maman a écrit :
Hello,
I have added a tool in my local instance to map BAM files on reference
genome fasta file thanks to BWA.
This tool runs, and the output file generated in database/files/000 is
correct (not empty and good data inside) but the output listed in the
history panel of Galaxy interface , is empty.
Could you please help me ?
Here is my xml file:
tool id=BWA_aln_sampe name= BWA with BAM files
descriptionBWA mapping BAM files on reference genome fasta
file/description
command interpreter=perlbwa_aln_sampe.pl $input1 $input2 $output1
/command
inputs
param format=fasta name=input1 type=data label=Reference
genome from your history - fasta file/
param format=bam name=input2 type=data label=Bam file/
/inputs
outputs
data format=bam name=output1 /
/outputs
help
This tool map BAM files on a reference genome.
/help
/tool
Here is my perl file :
#!/usr/bin/perl -w
use strict;
use File::Basename;
my $input_ref_genome = $ARGV[0];
my $input_bam = $ARGV[1];
my $output_bam = $ARGV[2];
my $input_dir=dirname($input_bam);
my $input_basename=basename($input_bam,'.bam');
my $input_bamsorted=$input_dir/${input_basename}-sorted;
#Ouverture des fichiers entrants
open (IN, $input_ref_genome) or die Cannot open $input_ref_genome !;
open (IN, $input_bam) or die Cannot open $input_bam !;
#Indexation du genome de reference
#system(bwa index $input_ref_genome ./bwa.log 21);
#Tri par nom du bam entrant pour travailler sur des donnees pairees
system(samtools sort -n $input_bam $input_bamsorted ./samtools.log
21);
#Alignement des donnees pairees uniquement
system(bwa aln $input_ref_genome -b1 ${input_bamsorted}.bam
${input_bamsorted}-1.sai ./bwaaln.log 21);
system(bwa aln $input_ref_genome -b2 ${input_bamsorted}.bam
${input_bamsorted}-2.sai ./bwaaln.log 21);
#bwa sampe
system(bwa sampe $input_ref_genome ${input_bamsorted}-1.sai
${input_bamsorted}-2.sai ${input_bamsorted}.bam ${input_bamsorted}.bam
| samtools view -bS - $output_bam ./bwa.log 21);
close( IN );
close( IN );
Thanks in advance,
Sarah
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[galaxy-dev] Tool added / pb with output file
Hello,
I have added a tool in my local instance to map BAM files on reference
genome fasta file thanks to BWA.
This tool runs, and the output file generated in database/files/000 is
correct (not empty and good data inside) but the output listed in the
history panel of Galaxy interface , is empty.
Could you please help me ?
Here is my xml file:
tool id=BWA_aln_sampe name= BWA with BAM files
descriptionBWA mapping BAM files on reference genome fasta
file/description
command interpreter=perlbwa_aln_sampe.pl $input1 $input2 $output1
/command
inputs
param format=fasta name=input1 type=data label=Reference
genome from your history - fasta file/
param format=bam name=input2 type=data label=Bam file/
/inputs
outputs
data format=bam name=output1 /
/outputs
help
This tool map BAM files on a reference genome.
/help
/tool
Here is my perl file :
#!/usr/bin/perl -w
use strict;
use File::Basename;
my $input_ref_genome = $ARGV[0];
my $input_bam = $ARGV[1];
my $output_bam = $ARGV[2];
my $input_dir=dirname($input_bam);
my $input_basename=basename($input_bam,'.bam');
my $input_bamsorted=$input_dir/${input_basename}-sorted;
#Ouverture des fichiers entrants
open (IN, $input_ref_genome) or die Cannot open $input_ref_genome !;
open (IN, $input_bam) or die Cannot open $input_bam !;
#Indexation du genome de reference
#system(bwa index $input_ref_genome ./bwa.log 21);
#Tri par nom du bam entrant pour travailler sur des donnees pairees
system(samtools sort -n $input_bam $input_bamsorted ./samtools.log
21);
#Alignement des donnees pairees uniquement
system(bwa aln $input_ref_genome -b1 ${input_bamsorted}.bam
${input_bamsorted}-1.sai ./bwaaln.log 21);
system(bwa aln $input_ref_genome -b2 ${input_bamsorted}.bam
${input_bamsorted}-2.sai ./bwaaln.log 21);
#bwa sampe
system(bwa sampe $input_ref_genome ${input_bamsorted}-1.sai
${input_bamsorted}-2.sai ${input_bamsorted}.bam ${input_bamsorted}.bam |
samtools view -bS - $output_bam ./bwa.log 21);
close( IN );
close( IN );
Thanks in advance,
Sarah
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[galaxy-dev] DrmCommunicationException: code 2: unable to contact qmaster using port 6444 on host login
Hello Galaxy group, I did not achieve to run again my Galaxy local instance. The error is: galaxy.jobs DEBUG 2012-06-28 11:57:36,785 Loaded job runner: galaxy.jobs.runners.local:LocalJobRunner Traceback (most recent call last): File /usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py, line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File /usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/app.py, line 124, in __init__ self.job_manager = jobs.JobManager( self ) File /usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 44, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File /usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 1190, in __init__ self._load_plugin( name ) File /usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py, line 1207, in _load_plugin self.job_runners[name] = runner( self.app ) File /usr/local/bioinfo/src/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py, line 100, in __init__ self.ds.initialize() File /usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/__init__.py, line 274, in init ialize _w.init(contactString) File /usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/wrappers.py, line 59, in init return _lib.drmaa_init(contact, error_buffer, sizeof(error_buffer)) File /usr/local/bioinfo/src/galaxy/galaxy-dist/eggs/drmaa-0.4b3-py2.6.egg/drmaa/errors.py, line 90, in error_c heck raise _ERRORS[code-1](code %s: %s % (code, error_buffer.value)) DrmCommunicationException: code 2: unable to contact qmaster using port 6444 on host login I didn't find an answer here: http://gmod.827538.n3.nabble.com/Galaxy-Hang-after-DrmCommunicationException-td3651225.html Could you please help me ? Thanks in advance, Sarah Maman ___ 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] MarkupSafe cannot be fetched
Hello, To solve this warning, python used by Galaxy is now localized on our server. I no longer use python available on our cluster. Thus, if python version on the cluster evolves, it will not impact Galaxy. Thanks to this modification, your script fetch_eggs.py have been start and some eggs have been updated except for Markupsafe. So I downloaded Markupsafe from Python website. Since then I have no warning on my runs ;-) Thanks, Sarah Nate Coraor a écrit : On Apr 27, 2012, at 6:00 AM, Sarah Maman wrote: Hello, After pulling latest changes (March 2012 - r 40f1816d6857), jobs launched run properly (output files OK) but I get the following warning: /WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched/ Hi Sarah, I'm guessing that you are using a cluster with Galaxy. If this is correct, please try the following: 1. Log in to a cluster node as the user that runs Galaxy 2. cd to the galaxy-dist directory 3. run `python ./scripts/fetch_eggs.py` This should grab any missing eggs. In addition, Galaxy GUI is not exactly GUI seen in the cloud (https://main.g2.bx.psu.edu/). For example, Visualization menu is absent and I think it should be related to the previous warning? See the 'enable_tracks' setting in universe_wsgi.ini to enable the Visualization menu. --nate How to ensure that eggs be properly fetched? Thank you in advance, Sarah Maman ___ 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] MarkupSafe cannot be fetched
Thank Nate for your help. Visualization menu is now effective. However, I still have the problem of updating eggs. Indeed, galaxy is installed on a virtual machine and jobs run on SGE cluster. But I have been discouraged by my system administrator to run fetch_eggs.py scripts from our cluster node. If I run `python ./scripts/fetch_eggs.py` in galaxy-dist directory, as Galaxy user, but on my virtual machine, missing eggs are not grabed. Do you have another solution? Thanks, Sarah Nate Coraor a écrit : On Apr 27, 2012, at 6:00 AM, Sarah Maman wrote: Hello, After pulling latest changes (March 2012 - r 40f1816d6857), jobs launched run properly (output files OK) but I get the following warning: /WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched/ Hi Sarah, I'm guessing that you are using a cluster with Galaxy. If this is correct, please try the following: 1. Log in to a cluster node as the user that runs Galaxy 2. cd to the galaxy-dist directory 3. run `python ./scripts/fetch_eggs.py` This should grab any missing eggs. In addition, Galaxy GUI is not exactly GUI seen in the cloud (https://main.g2.bx.psu.edu/). For example, Visualization menu is absent and I think it should be related to the previous warning? See the 'enable_tracks' setting in universe_wsgi.ini to enable the Visualization menu. --nate How to ensure that eggs be properly fetched? Thank you in advance, Sarah Maman ___ 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] Interested in speaking with other, institutions deploying Galaxy locally?
Hello, This is a great idea. I'm interested. Thanks ! Sarah Maman -- Message: 1 Date: Fri, 27 Apr 2012 13:45:16 -0500 From: Ann Black-Ziegelbein annbl...@eng.uiowa.edu To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally? Message-ID: 4f9ae93c.20...@eng.uiowa.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi everyone - Here at the University of Iowa we are working on deploying Galaxy locally for campus wide access. I am interested in forming a community of other institutions trying to deploy Galaxy locally and mange/operate it on a broad level. Is anyone else? If there is enough interest, possibly we could have a community conference call every other month to have an open discussion on how we are all deploying galaxy, customizations we are making, problems we are encountering, bugs, and any add-on operations management for galaxy being developed, etc. Would love to hear from others operating Galaxy or in process of standing up a local deployment. Thanks! Ann Black-Ziegelbein ___ 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] MarkupSafe cannot be fetched
Hello, After pulling latest changes (March 2012 - r 40f1816d6857), jobs launched run properly (output files OK) but I get the following warning: /WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched/ In addition, Galaxy GUI is not exactly GUI seen in the cloud (https://main.g2.bx.psu.edu/). For example, Visualization menu is absent and I think it should be related to the previous warning? How to ensure that eggs be properly fetched? Thank you in advance, Sarah Maman ___ 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 version / Mercurial
Thank you very much Dannon, it works. The more I discover Galaxy, the more I appreciate its use. Again, thank Galaxy team for this great tool. Sarah Maman Dannon Baker a écrit : Hi Sarah, You should be able to do this with the -r option of the clone command, so: `hg clone -r b258de1e6cea https://bitbucket.org/galaxy/galaxy-dist`. -Dannon On Apr 25, 2012, at 3:08 AM, Sarah Maman wrote: Hello, I would like to get source code with Mercurial of this tarballs : galaxy-dist.b258de1e6cea.tar.gz, and not the latest source. Is it possible to specify b258de1e6cea version with hg clone command ? The aim is to update my copy of Galaxy wich have been locally installed with a tarball in order to use, in the future, Mercurial and hg pull to update Galaxy version. Thanks a lot, Sarah Maman From: Sarah Maman sarah.ma...@toulouse.inra.fr Subject: Galaxy version Date: April 24, 2012 10:23:01 AM EDT To: Nate Coraor n...@bx.psu.edu, galaxy-dev-requ...@lists.bx.psu.edu Hello, I would like to get source code with Mercurial of this tarballs : galaxy-dist.b258de1e6cea.tar.gz, and not the latest source. Is it possible to specify b258de1e6cea version with hg clone command ? The aim is to update my copy of Galaxy wich have been locally installed with a tarball in order to use, in the future, Mercurial and hg pull to update Galaxy version. Thanks a lot, Sarah Maman ___ 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] Display galaxy variable
Hello,
In a Galaxy tool, I would like to display a pre-completed path in the
xml inputbox, inside the tool.xml file.
Consequently, I would like to add a variable in an param value= /
tag , like this :
tool id=test name=test version=
command interpreter=shtest.sh $in $out/command
inputs
param name=filepath type=text size=100 value=/work/$out /
/inputs
...
and in test.sh : $out is defined to be ${trans.user.username}
Do you have any idea to display ${trans.user.username} variable in
order to be shown in galaxy interface (gui) thanks to xml file ?
I achieve to display ${trans.user.username} in
/templates/root/tool_menu.mako but not in the xml file.
Thanks in advance,
Sarah
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Re: [galaxy-dev] LDAP authentification
Thanks nate,
I just would like to share others informations :
* I have added a VirtualHost, proxy and a DocumentRoot
* Consequently, RewriteRule have been modified :
Remplace
RewriteRule ^ galaxy/ (. *) http://ip:port $ 1 [P]
by
RewriteRule ^ / (. *) http://ip:port/ $ 1 [P]
It should be better for security.
Faithfully,
Sarah Maman
Nate Coraor a écrit :
On Feb 13, 2012, at 7:38 AM, Sarah Maman wrote:
Hello,
I managed to connect to Galaxy to LDAP ;-)
Three points were blocking for me:
* Being root of my virtual machine can carry out tests
* I confused login / password of two LDAP, so I thought that my authentication
method was not good while I was using the wrong password ...
* It is better not to go through a proxy
Hi Sarah,
Thanks very much for reporting back with your findings. This should be very
helpful for people who stumble on to similar problems in the future.
1 - Set configuration file of Galaxy: universe_wsgi.ini to delegate user
authentication to an upstream proxy Apache:
Users and Security
use_remote_user = True
remote_user_maildomain = toulouse.inra.fr
2 - Create a file type htaccess file named galaxy.conf (in / etc / httpd /
conf.d /):
For reasons of performance and safety, it is advisable not to use a. htaccess
but a galaxy.conf file in the main server configuration (Apache), because the
latter will be charged a once when the server starts. With an .htaccess file,
this file will be charged at each access.
RewriteEngine on
Location /galaxy
# Define the authentication method
AuthType Basic
AuthName Galaxy
AuthBasicProvider ldap
AuthLDAPURL ldap :/ / server URL: 389/...
AuthzLDAPAuthoritative off
Require valid-user
RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e
/ Location
RewriteRule ^ / $ galaxy / galaxy / [R]
RewriteRule ^ / galaxy / static / style / (. *) /
var/www/html/galaxy/static/june_2007_style/blue / $ 1 [L]
RewriteRule ^ / galaxy / static / scripts / (. *) /vVar / www / html / galaxy /
static / scripts / packed / $ 1 [L]
RewriteRule ^ / galaxy / static / (. *) / var / www / html / galaxy / static /
$ 1 [L]
RewriteRule ^ / galaxy / favicon.ico / var / www / html / galaxy / static /
favicon.ico [L]
RewriteRule ^ / galaxy / robots.txt / var / www / html / galaxy / static /
robots.txt [L]
RewriteRule ^ / galaxy (. *) http://ip:port $ 1 [P]
As Galaxy is not installed in root directory but in a galaxy directory (var /
www / html / galaxy /), so following changes are needed:
This is probably not a good idea. From the documentation:
Please note that Galaxy should never be located on disk inside Apache's
DocumentRoot. By default, this would expose all of Galaxy (including datasets)
to anyone on the web.
Galaxy is a proxied application and as such, only the static content like
javascript and images are served directly by Apache (and this is set up with
the RewriteRules), everything else is passed through to the Galaxy application
via a proxied http connection. Right now I could presumably use the URL
http://server/galaxy/galaxy-dist/database/files/000/dataset_1.dat to view a
dataset directly.
1 - Add a RewriteRule
2 - Do not go through a proxy
Can you clarify this? I'm a bit confused, since if you are connecting to
Apache to access Galaxy, you are going through a proxy.
3 - REMOTE_USER variable is AUTHENTICATE_uid ( AUTHENTICATE_ sAMAccountName for
Windows AD)
I've added this to the wiki page, thanks!
--nate
4 - To generate dynamic URLs, it is necessary to configure prefix in
universe_wsgi.ini :
[Filter: proxy-prefix]
use = egg: # prefix PasteDeploy
prefix = / galaxy
[App: main]
filter-with = proxy-prefix
cookie_path = / galaxy
If you are not root on the virtual machine, create a symlink from / etc / httpd
/ conf.d / to galaxy.conf
3 - Some useful checks
Verify Apache version and Apache modules because each directive must have an
associated module:
Directive → Related module (which mod_ldap)
AuthType → mod_auth_basic.so
AuthBasicProvider → mod_authnz_ldap and mod_authz_ldap
Rewrite (for proxy) → mod_rewrite.so
RequestHeader→ mod_headers
Check that the galaxy is installed on ldap using this command: ldapsearch-x-h LDAP URL :
port-b dc
When you make a modification in galaxy.conf, restart Apache (or graful).
In httpd.conf, so that access management is authorized by the file. #
# AccessFileName: The name of the file to look for in EACH directory
# For additional configuration directives. See also the AllowOverride
# Directive.
#
AccessFileName. Htaccess
Check: Chmod 777 galaxy.conf
4 - Finally, restart run.sh (sh run.sh )
Thanks A LOT for your help,
Sarah
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Re: [galaxy-dev] LDAP authentification
Hello,
I managed to connect to Galaxy to LDAP ;-)
Three points were blocking for me:
* Being root of my virtual machine can carry out tests
* I confused login / password of two LDAP, so I thought that my
authentication method was not good while I was using the wrong password ...
* It is better not to go through a proxy
1 - Set configuration file of Galaxy: universe_wsgi.ini to delegate user
authentication to an upstream proxy Apache:
Users and Security
use_remote_user = True
remote_user_maildomain = toulouse.inra.fr
2 - Create a file type htaccess file named galaxy.conf (in / etc /
httpd / conf.d /):
For reasons of performance and safety, it is advisable not to use a.
htaccess but a galaxy.conf file in the main server configuration
(Apache), because the latter will be charged a once when the server
starts. With an .htaccess file, this file will be charged at each access.
RewriteEngine on
Location /galaxy
# Define the authentication method
AuthType Basic
AuthName Galaxy
AuthBasicProvider ldap
AuthLDAPURL ldap :/ / server URL: 389/...
AuthzLDAPAuthoritative off
Require valid-user
RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e
/ Location
RewriteRule ^ / $ galaxy / galaxy / [R]
RewriteRule ^ / galaxy / static / style / (. *) /
var/www/html/galaxy/static/june_2007_style/blue / $ 1 [L]
RewriteRule ^ / galaxy / static / scripts / (. *) /vVar / www / html /
galaxy / static / scripts / packed / $ 1 [L]
RewriteRule ^ / galaxy / static / (. *) / var / www / html / galaxy /
static / $ 1 [L]
RewriteRule ^ / galaxy / favicon.ico / var / www / html / galaxy /
static / favicon.ico [L]
RewriteRule ^ / galaxy / robots.txt / var / www / html / galaxy / static
/ robots.txt [L]
RewriteRule ^ / galaxy (. *) http://ip:port $ 1 [P]
As Galaxy is not installed in root directory but in a galaxy directory
(var / www / html / galaxy /), so following changes are needed:
1 - Add a RewriteRule
2 - Do not go through a proxy
3 - REMOTE_USER variable is AUTHENTICATE_uid ( AUTHENTICATE_
sAMAccountName for Windows AD)
4 - To generate dynamic URLs, it is necessary to configure prefix in
universe_wsgi.ini :
[Filter: proxy-prefix]
use = egg: # prefix PasteDeploy
prefix = / galaxy
[App: main]
filter-with = proxy-prefix
cookie_path = / galaxy
If you are not root on the virtual machine, create a symlink from / etc
/ httpd / conf.d / to galaxy.conf
3 - Some useful checks
Verify Apache version and Apache modules because each directive must
have an associated module:
Directive → Related module (which mod_ldap)
AuthType → mod_auth_basic.so
AuthBasicProvider → mod_authnz_ldap and mod_authz_ldap
Rewrite (for proxy) → mod_rewrite.so
RequestHeader→ mod_headers
Check that the galaxy is installed on ldap using this command:
ldapsearch-x-h LDAP URL : port-b dc
When you make a modification in galaxy.conf, restart Apache (or graful).
In httpd.conf, so that access management is authorized by the file. #
# AccessFileName: The name of the file to look for in EACH directory
# For additional configuration directives. See also the AllowOverride
# Directive.
#
AccessFileName. Htaccess
Check: Chmod 777 galaxy.conf
4 - Finally, restart run.sh (sh run.sh )
Thanks A LOT for your help,
Sarah
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[galaxy-dev] Adding a new python tool
Hello, I managed to add a new tool coded in bash but I am having some difficulty adding a tool coded in python. Here are the contents of the test files: * Content of test.xml file in galaxy/galaxy-dist/tools/test/test.xml : tool id=test name=Test name descriptionTest description/description command interpreter=pythontest.py/command /tool * Content of test.py file in galaxy/galaxy-dist/tools/test/test.py : #!/usr/bin/python import os for param in os.environ.keys(): print %20s %s % (param,os.environ[param]) * Content of tool_conf_xml file in galaxy/galaxy-dist/ : ?xml version=1.0? toolbox section name=Get Data id=getext tool file=test/test.xml / tool file=uploadFile/uploadFile.xml / tool file=data_source/upload.xml/ tool file=data_source/ucsc_tablebrowser.xml / tool file=data_source/ucsc_tablebrowser_test.xml /.. Could you, please, explain me why the new tool test isn't avalaible in Tools/Get Data windows (on the left, before uploadFile and upload tools ) ? Thanks in advance, Sarah ___ 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] LDAP authentification
Hi,
Thanks to log messages from remoteuser.py in
./lib/galaxy/web/framework/middleware/remoteuser.py:
print('affichage des variables d acces')
print ('self domain : %s'%self.maildomain)
print ('path info : %s'%path_info)
print ('admin user : %s' %self.admin_users)
http_remote_user = environ.get('HTTP_REMOTE_USER','')
print ('http remote user : %s'%http_remote_user)
remote_user = environ.get('REMOTE_USER', '')
print ('remote user :%s' %remote_user)
Galaxy prints every environment variable it receives, and I have seen
that HTTP_REMOTE_USER variable is (null).
Moreover, Galaxy is defined as a valid Proxy (reverse proxy ??) so
galaxy.conf is :
VirtualHost localhost:port
# Define Galaxy as a valid Proxy
Proxy localhost:port
Order deny,allow
Allow from all
RewriteEngine on
# 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]
# Set the REMOTE_USER header to the contents of the LDAP query
response's uid attribute
RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/static/style/(.*)
/usr/local/bioinfo/src/galaxy/galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/static/(.*)
/usr/local/bioinfo/src/galaxy/galaxy-dist/static/$1 [L]
RewriteRule ^/images/(.*)
/usr/local/bioinfo/src/galaxy/galaxy-dist/static/images/$1 [L]
RewriteRule ^/favicon.ico
/usr/local/bioinfo/src/galaxy/galaxy-dist/static/favicon.ico [L]
RewriteRule ^/favicon.ico /var/www/html/favicon.ico [L]
RewriteRule ^/robots.txt
/usr/local/bioinfo/src/galaxy/galaxy-dist/static/robots.txt [L]
RewriteRule ^(.*) localhost:port$1 [P]
/Proxy
Location /.
AuthType Basic
AuthBasicProvider ldap
AuthName Galaxy
AuthLDAPURL ldap://serveur ...
AuthzLDAPAuthoritative on
Require valid-user
/Location
/VirtualHost
But, I didn't achieve, yet , to access REMOTE_USER value throught proxy.
In universe_wsgi.ini,
*use_remote_user = True*
and
*remote_user_maildomain = toulouse.inra.fr*
Thanks in advance,
Sarah
Nate Coraor a écrit :
On Jan 19, 2012, at 10:49 AM, Sarah Maman wrote:
Hi Brad, Hi Christopher,
Thanks a lot.
I'm talking to Open LDAP. I have changed
RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e
to
RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e
But I always have the same message /(Access to Galaxy is denied
Galaxy is configured to authenticate users via an external method (such as HTTP
authentication in Apache), but a username was not provided by the upstream
(proxy) server. This is generally due to a misconfiguration in the upstream
server. )/
Hi Sarah,
This configuration will need to be in your Apache config (the location of which
varies depending on your OS and/or how Apache is installed) rather than an
.htaccess file.
--nate
This is my .conf file :
Proxy http://localhost:8080
Order deny,allow
Allow from all
/Proxy
RewriteEngine on
Location /
AuthType Basic
AuthName Galaxy
AuthBasicProvider ldap
AuthLDAPURL
ldap://server/ou=People,ou=genopole,ou=toulouse,o=inra,c=fr?u
id?sub?(objectClass=person)
AuthzLDAPAuthoritative off
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
RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e
/Location
Thanks in advance,
Sarah
Langhorst, Brad a écrit :
Hi Sarah:
I don't know what kind of LDAP you're talking to... I'm talking to Active
Directory and this configuration works in that situation.
Order allow,deny
allow from all
AuthType Basic
AuthName NEB Credentials
AuthBasicProvider ldap
AuthzLDAPAuthoritative off
AuthLDAPBindDN ccaloo...@neb.com
AuthLDAPBindPassword password
AuthLDAPURL
ldap://ldap.domain.com:389/dc=domain,dc=com?sAMAccountName
require valid-user
RewriteCond %{IS_SUBREQ} ^false$
RewriteCond %{LA-U:REMOTE_USER} (.+)
RewriteRule . - [E=RU:%1]
RequestHeader set REMOTE_USER
%{AUTHENTICATE_sAMAccountName}e
[galaxy-dev] Unix user account/connection and Galaxy connection
Dear all, There is currently no link between an user ssh connection on his own account (own space on Unix) and the Galaxy connection. How to run Galaxy on an Unix user account? How to link the data storage system and the Unix user account (symlink?)? The goal is to not need to copy or move data. PS : Thanks a lot to David, Gordon, Brad, Christophe and Nate for your help on LDAP authentification. I always try to find a solution (Apache configuration). I will inform Galaxy list when I will find a solution. Thanks in advance, Sarah ___ 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] LDAP authentification
Hello,
I'm trying to install galaxy on a apache server,and i have the same
error message than David HOOVER when i tried to generate the
authentification files. Thanks to David Hoover who gives me some helpful
explanation.
When i read the thread on gmod, it seems,that the problem is solved
(http://gmod.827538.n3.nabble.com/trouble-with-authentication-through-Apache-td1809681.html
http://gmod.827538.n3.nabble.com/trouble-with-authentication-through-Apache-td1809681.html)
but I did not find the solution in my case.
I use LDAP authentification and Galaxy is implemented on a VM.
Could you please explain me how to solve it. I really need help.
I modified universe file ( in galaxy-dist) and i created .htaccess file
in galaxy-dist/ :
* in universe_wsgi.ini:
use_remote_user = True
remote_user_maildomain = example.org http://example.org
* in .htaccess file in galaxy-dist/ Directory :
1
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_1
# Define Galaxy as a valid Proxy
2
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_2
Proxy http://localhost:8080
3
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_3
Order deny,allow
4
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_4
Allow from all
5
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_5
/Proxy
6
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_6
#!highlight apache
7
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_7
Location /
8
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_8
AuthType Basic
9
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_9
AuthBasicProvider *ldap*
10
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_10
Auth*LDAP*URL
*ldap*://server:389/ou=People,dc=example,dc=org?uid?sub?(objectClass=person)
11
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_11
Authz*LDAP*Authoritative off
12
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_12
Require valid-user
13
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_13
# Set the REMOTE_USER header to the contents of the *LDAP* query response's
uid attribute
14
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_14
RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e
15
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy?highlight=%28Ldap%29#CA-e07a9dbbf4f816c0970d4995f4abb957a6683638_15
/Location
with location, AuthBasicProvider and proxy competed
But i have the error :
Access to Galaxy is denied
Galaxy is configured to authenticate users via an external method (such
as HTTP authentication in Apache), but a username was not provided by
the upstream (proxy) server. This is generally due to a misconfiguration
in the upstream server.
Thank you, and best regards
Sarah Maman
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Re: [galaxy-dev] LDAP authentification
Hi Brad, Hi Christopher,
Thanks a lot.
I'm talking to Open LDAP. I have changed
RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e
to
RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e
But I always have the same message /(Access to Galaxy is denied
Galaxy is configured to authenticate users via an external method (such
as HTTP authentication in Apache), but a username was not provided by
the upstream (proxy) server. This is generally due to a misconfiguration
in the upstream server. )/
This is my .conf file :
Proxy http://localhost:8080
Order deny,allow
Allow from all
/Proxy
RewriteEngine on
Location /
AuthType Basic
AuthName Galaxy
AuthBasicProvider ldap
AuthLDAPURL
ldap://server/ou=People,ou=genopole,ou=toulouse,o=inra,c=fr?u
id?sub?(objectClass=person)
AuthzLDAPAuthoritative off
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
RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e
/Location
Thanks in advance,
Sarah
Langhorst, Brad a écrit :
Hi Sarah:
I don't know what kind of LDAP you're talking to... I'm talking to Active
Directory and this configuration works in that situation.
Order allow,deny
allow from all
AuthType Basic
AuthName NEB Credentials
AuthBasicProvider ldap
AuthzLDAPAuthoritative off
AuthLDAPBindDN ccaloo...@neb.com
AuthLDAPBindPassword password
AuthLDAPURL
ldap://ldap.domain.com:389/dc=domain,dc=com?sAMAccountName
require valid-user
RewriteCond %{IS_SUBREQ} ^false$
RewriteCond %{LA-U:REMOTE_USER} (.+)
RewriteRule . - [E=RU:%1]
RequestHeader set REMOTE_USER
%{AUTHENTICATE_sAMAccountName}e
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[galaxy-dev] Information about server availability
Dear all, I would like to get the latest copy from the repository (https://bitbucket.org/galaxy/galaxy-dist) in order to install Galaxy. But, unfortunatly, no server is available to handle this request (503 Service Unavailable). Could you, please, help me ? Do you know when this information will be available ? Please, excuse me if this information is available on your web and if I have not seen it. Happy new year, Sarah Maman -- Sarah Maman INRA - LCG - SIGENAE Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Tax: +33(0)5.61.28.57.53 ___ 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/
