Re: [galaxy-dev] secure Galaxy with SSL
Hello Jim Re your problem #1 (UCSC browser appears to be blocked), I've seen something similar with our local Galaxy instance, which is also served via https. In our case I believe this is actually a browser issue: the latest version of Firefox silently blocks mixed secure and insecure content: https://blog.mozilla.org/tanvi/2013/04/10/mixed-content-blocking-enabled-in-firefox-23/ (I think Chrome and IE do something similar, although IE at least gives a warning.) The workaround is either to disable mixed content blocking (not trivial in Firefox, and probably not a good idea in general), or to do something like e.g. right-click Open link in new tab on the Get data/UCSC main table browser link in Galaxy. Once UCSC has loaded in the new tab it can be used to send data back to Galaxy without any problems. HTH Best wishes, Peter On 18/11/13 23:03, Jingchao Zhang wrote: Dear all, Today I installed the SSL module for our local Galaxy instance and the https://; link is working fine. I added this Location/ RequestHeader set X-URL-SCHEME https /Location in our Apache configuration file as instructed in this webpage: http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy Here are my problems with SSL: 1. Some build in links like UCSC Main http://genome.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=https%3A//hcc-galaxy.unl.edu/tool_runnertool_id=ucsc_table_direct1hgta_compressType=nonesendToGalaxy=1hgta_outputType=bed table browser and UCSC Test http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=https%3A//hcc-galaxy.unl.edu/tool_runnertool_id=ucsc_table_direct_test1hgta_compressType=nonesendToGalaxy=1hgta_outputType=bed table browser become invalid. If I click on them, nothing will happen, as if they are blocked. 2. The old http link still works, which I think shouldn't because I added the RequestHeader ... https line in Apache configuration. I really want to disable the http link because the new users could be easily led to the old one. Both httpd and Galaxy have been restarted after the changes are made. Since I didn't find any similar threads in the mailist, I hope someone here can help me out with this. Thanks, Jim ___ 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/ -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___ 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] Empty tool panel
Hi, my mistake... I got an error in the apache proxy configuration. The funny thing is that everything seemed to work excepted the tool panel menu which was empty. Sorry for that and thanks. Yec'han Dr. Yec'han LAIZET Ingenieur Bioinformatique Tel: +33 (0)5 57 12 27 75 _ Plateforme Genome Transcriptome INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS Le 15/11/2013 23:45, Jeremy Goecks a écrit : Do you see any errors in the JavaScript console? Does this only happen on particular Web browsers? J. On Nov 15, 2013, at 10:15 AM, Yec'han Laizet ylai...@pierroton.inra.fr wrote: Hi, In the current version of galaxy stable branch (5c789ab4144a), the tool panel is empty when installed (freshly and out of the box) on my production server (ubuntu server 12.04). If I copy this galaxy folder onto my laptop, the tool panel shows up (ubuntu 13.10). Do you have an idea of what could be the problem? Thanks Yec'han Dr. Yec'han LAIZET Ingenieur Bioinformatique Tel: +33 (0)5 57 12 27 75 _ Plateforme Genome Transcriptome INRA-UMR BIOGECO 1202 Equipe Genetique 69 route d'Arcachon 33612 CESTAS ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Status of GATK in Galaxy
Hi, I found that the GATK tools do not have the same requirement tag. For example indel-realigner has version 1.4, realigner_target_creator has version 1.3. Is that correct? What is the recent version that is required for GATK? Also realigner_target_creator uses the gatk_picard_indexes location file, but under tool-data is only a gatk_sorted_picard_indexes.loc file. Are there any concrete plans for the GATK wrappers. Especially to update to a newer version. Or is that not feasible because of this complicated license policy and the phone-home option ... I found the following trello card, but its a little bit outdated: https://trello.com/c/IPkT2spd Is anyone running a recent GATK version in Galaxy? Thanks! Bjoern ___ 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] Status of GATK in Galaxy
Hi, I have GATK 2.4 running in our local galaxy, next to the default galaxy 1.x version. Both are in the tool menu, but only users that have provided a licence or proof that they are from an academic site have access to the 2.4 version. This is based on a usergroup check in a dynamic job runner configuration. I used modified the GATK 2 tool configuration from the test toolshed (by jjohnson). Modifications to the xmls included: --max_jvm_heap xG instead of --max_jvm_heap_fraction 1 : we use shared nodes, so it's not allowed to use all ram. --num_threads : some hard coded thread settings were changed made sure the '--et 'NO_ET' is commented out, as we don't have a key. relevant dynamic_runner part: from galaxy.jobs.mapper import JobMappingException if 'gatk2' in tool_id = 0: user_group_assocs = user.groups or [] user_has_license = 'gatk2_license' in [user_group_assoc.group.name for user_group_assoc in user_group_assocs] if not user_has_license: raise JobMappingException(GATKv2 is only available to non-profit, academic users. Please send a mail to geert.vandewey...@uantwerpen.be to confirm this.) Best, Geert On 11/19/2013 12:26 PM, Bjoern Gruening wrote: Hi, I found that the GATK tools do not have the same requirement tag. For example indel-realigner has version 1.4, realigner_target_creator has version 1.3. Is that correct? What is the recent version that is required for GATK? Also realigner_target_creator uses the gatk_picard_indexes location file, but under tool-data is only a gatk_sorted_picard_indexes.loc file. Are there any concrete plans for the GATK wrappers. Especially to update to a newer version. Or is that not feasible because of this complicated license policy and the phone-home option ... I found the following trello card, but its a little bit outdated: https://trello.com/c/IPkT2spd Is anyone running a recent GATK version in Galaxy? Thanks! Bjoern ___ 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/ -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer ___ 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] secure Galaxy with SSL
Hi Peter, Thanks so much for your help! It is like you said a browser issue. I also noticed that the Galaxy main server (https://usegalaxy.org/) doesn't have this problem. And their USCS main table browser uses https instead of http. Does anyone know why this isn't included in the current Galaxy release? And how can I change my current http USCS main to https USCS main? Thanks, Jim Message: 8 Date: Tue, 19 Nov 2013 08:51:03 + From: Peter Briggs peter.bri...@manchester.ac.uk To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] secure Galaxy with SSL Message-ID: 528b2677.9050...@manchester.ac.uk Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hello Jim Re your problem #1 (UCSC browser appears to be blocked), I've seen something similar with our local Galaxy instance, which is also served via https. In our case I believe this is actually a browser issue: the latest version of Firefox silently blocks mixed secure and insecure content: https://blog.mozilla.org/tanvi/2013/04/10/mixed-content-blocking-enabled-in-firefox-23/ (I think Chrome and IE do something similar, although IE at least gives a warning.) The workaround is either to disable mixed content blocking (not trivial in Firefox, and probably not a good idea in general), or to do something like e.g. right-click Open link in new tab on the Get data/UCSC main table browser link in Galaxy. Once UCSC has loaded in the new tab it can be used to send data back to Galaxy without any problems. HTH Best wishes, Peter On 18/11/13 23:03, Jingchao Zhang wrote: Dear all, Today I installed the SSL module for our local Galaxy instance and the https://; link is working fine. I added this Location/ RequestHeader set X-URL-SCHEME https /Location in our Apache configuration file as instructed in this webpage: http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy Here are my problems with SSL: 1. Some build in links like UCSC Main http://genome.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=https%3A//hcc-galaxy.unl.edu/tool_runnertool_id=ucsc_table_direct1hgta_compressType=nonesendToGalaxy=1hgta_outputType=bed table browser and UCSC Test http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=https%3A//hcc-galaxy.unl.edu/tool_runnertool_id=ucsc_table_direct_test1hgta_compressType=nonesendToGalaxy=1hgta_outputType=bed table browser become invalid. If I click on them, nothing will happen, as if they are blocked. 2. The old http link still works, which I think shouldn't because I added the RequestHeader ... https line in Apache configuration. I really want to disable the http link because the new users could be easily led to the old one. Both httpd and Galaxy have been restarted after the changes are made. Since I didn't find any similar threads in the mailist, I hope someone here can help me out with this. Thanks, Jim ___ 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/ -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___ 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] Next GalaxyAdmins Meetup: November 20
Hello all, Just a reminder that there is a GalaxyAdmins meetup on Wednesday November 20 (tomorrow) at 10am US Central time. See http://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2013_11_20 Nate Coraor will talk about the move of usegalaxy.org to TACC, and Srinivas and myself will talk about followup to the GalaxyAdmins Birds-of-a-feather session at GCC2013. Take a look at these two draft implementations of action items from that discussion: 1. Galaxy Deployment Pageshttp://wiki.galaxyproject.org/Community/Deployments 2. Galaxy Log Pages http://wiki.galaxyproject.org/Community/Logs Please come prepared to discuss what you would like to see in these pages, and make suggestions on how to make it easy to create these documents. Finally, it takes a few minutes to connect to the meetup technology. Please give yourself 5 or 10 minutes in advance to connect. Thanks, Dave C On Thu, Nov 14, 2013 at 12:00 AM, Dave Clements cleme...@galaxyproject.orgwrote: Hello all, The next GalaxyAdmins meetup will be Wednesday, November 20, at 10am US Central time. See the meetup pagehttp://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2013_11_20 for a link and directions for connecting to the meetup. *GCC2013 GalaxyAdmins BoF Followup* This is our first meetup since the GCC2013 GalaxyAdmins BoFhttp://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyAdmins where we discussed what the group should focus on going forward, and what the Galaxy Project can do to support the group. As suggested at GCC2013, followup to that discussion will be the main topic for this meetup. We came out with several action items and one piece of unfinished business (leadership). Also, as suggested at the GCC2013 BoF, we would like to encourage discussion in the week before the meetup. Therefore, 1. Please review the notes from the GCC2013 GalaxyAdmins BoFhttp://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyAdmins 2. Take a look at these two draft implementations of action items from that discussion: 1. Galaxy Deployment Pageshttp://wiki.galaxyproject.org/Community/Deployments 2. Galaxy Log Pages http://wiki.galaxyproject.org/Community/Logs And, if you see anything that you want to comment on please reply to this thread on the Galaxy-Dev list. I'll update other actions as the call gets closer. *Galaxy Project Update: Main moves to TACC* Nate Coraor will give the project update, focusing on the recent move of UseGalaxy.org to TACC. We hope to see (well, hear) you there, and please don't hesitate to ask if you have any questions. Thanks, Dave C. -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] secure Galaxy with SSL
On Tue, Nov 19, 2013 at 12:32 PM, Jingchao Zhang zh...@unl.edu wrote: Hi Peter, Thanks so much for your help! It is like you said a browser issue. I also noticed that the Galaxy main server (https://usegalaxy.org/) doesn't have this problem. And their USCS main table browser uses https instead of http. Does anyone know why this isn't included in the current Galaxy release? And how can I change my current http USCS main to https USCS main? Hi Jim, We did this for usegalaxy.org simply by locally changing the URL in the tool's config from http to https. A proper fix for this tool (and other external sites which open in the center iframe) is in the works and will be released to the stable branch once it's done. --nate Thanks, Jim Message: 8 Date: Tue, 19 Nov 2013 08:51:03 + From: Peter Briggs peter.bri...@manchester.ac.uk To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] secure Galaxy with SSL Message-ID: 528b2677.9050...@manchester.ac.uk Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hello Jim Re your problem #1 (UCSC browser appears to be blocked), I've seen something similar with our local Galaxy instance, which is also served via https. In our case I believe this is actually a browser issue: the latest version of Firefox silently blocks mixed secure and insecure content: https://blog.mozilla.org/tanvi/2013/04/10/mixed-content-blocking-enabled-in-firefox-23/ (I think Chrome and IE do something similar, although IE at least gives a warning.) The workaround is either to disable mixed content blocking (not trivial in Firefox, and probably not a good idea in general), or to do something like e.g. right-click Open link in new tab on the Get data/UCSC main table browser link in Galaxy. Once UCSC has loaded in the new tab it can be used to send data back to Galaxy without any problems. HTH Best wishes, Peter On 18/11/13 23:03, Jingchao Zhang wrote: Dear all, Today I installed the SSL module for our local Galaxy instance and the https://; link is working fine. I added this Location/ RequestHeader set X-URL-SCHEME https /Location in our Apache configuration file as instructed in this webpage: http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy Here are my problems with SSL: 1. Some build in links like UCSC Main http://genome.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=https%3A//hcc-galaxy.unl.edu/tool_runnertool_id=ucsc_table_direct1hgta_compressType=nonesendToGalaxy=1hgta_outputType=bed table browser and UCSC Test http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=https%3A//hcc-galaxy.unl.edu/tool_runnertool_id=ucsc_table_direct_test1hgta_compressType=nonesendToGalaxy=1hgta_outputType=bed table browser become invalid. If I click on them, nothing will happen, as if they are blocked. 2. The old http link still works, which I think shouldn't because I added the RequestHeader ... https line in Apache configuration. I really want to disable the http link because the new users could be easily led to the old one. Both httpd and Galaxy have been restarted after the changes are made. Since I didn't find any similar threads in the mailist, I hope someone here can help me out with this. Thanks, Jim ___ 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/ -- Peter Briggs peter.bri...@manchester.ac.uk Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] wigTobigwig error: broken pipe and len file not found
Hi Nate, Thanks for the note! So may I ask whether this is expected? I mean, the len_file_path points to tool-data/..., which is right inside galaxy-dist, and it is natural. I didn't realize that this path is relative to the individual job working dir. Are there any other similar cases? Best, Rui On Mon, Nov 18, 2013 at 10:40 AM, Nate Coraor n...@bx.psu.edu wrote: On Sat, Nov 16, 2013 at 12:27 PM, ruiwang.sz ruiwang...@gmail.com wrote: Hi All, I‘m seeing some weird error messages...I googled but didn't see anything useful: So, it is during the wigToBigwig conversion: Dataset generation errors Dataset 47: Wig/BedGraph-to-bigWig on data 43 Tool execution generated the following error message: grep: writing output: Broken pipe grep: writing output: Broken pipe grep: writing output: Broken pipe and many more lines of the same error The tool produced the following additional output: Couldn't open tool-data/shared/ucsc/chrom/mm10.len , No such file or directory but it is there: ls -l tool-data/shared/ucsc/chrom/mm10.len -rw-rw-r-- 1 bioinfoadmin bioinfoadmin 1405 Oct 9 11:33 tool-data/shared/ucsc/chrom/mm10.len Hi Rui, Jobs run in a working directory based on the job id under whatever is configured as job_working_directory in universe_wsgi.ini. Thus, from that directory, tool-data/shared/ ... does not exist. To fix this, set len_file_path in universe_wsgi.ini to an absolute path. --nate From the Galaxy server log, I found these: galaxy.tools WARNING 2013-11-15 17:46:43,200 Failed to resolve dependency on 'ucsc_tools', ignoring galaxy.jobs.runners.local DEBUG 2013-11-15 17:46:43,255 (216) executing: grep -v ^track /home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_458.dat | wigToBigWig stdin tool-data/shared/ucsc/chrom/mm10.len /home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_473.dat -blockSize=256 -itemsPerSlot=1024 -clip 21 || echo Error running wigToBigWig. 2 and then, setmetadata set the dataset state to ERROR. I did verify that the result dataset_473.dat has a size 0. However, when I run the command alone: grep -v ^track /home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_458.dat | wigToBigWig stdin tool-data/shared/ucsc/chrom/mm10.len /home/bioinfoadmin/app/galaxy-dist/database/files/000/dataset_473.dat -blockSize=256 -itemsPerSlot=1024 -clip it successfully generated the dataset_473.dat. also, I look into the wig_to_Bigwig.xml in tools/filters, the command is: grep -v ^track $input1 | wigToBigWig stdin $chromInfo $out_file1 however, I don't see where this $chromInfo was defined, yet it indeed found the the correct value: tool-data/shared/ucsc/chrom/mm10.len. how does that happen? it is very puzzling...I'm not sure if anyone has seen this before, please let me know! Thanks, Rui ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Status of GATK in Galaxy
Hi Geert, thanks for the information. Are you running GATK-2.4 or GATK-Lite-2.4. As far I know the lite version is deprecated. JJ are your wrappers in bitbucket/github? If you agree I would try to migrate to a recent GATK version and implement GALAXY_SLOTS. Not sure about the installation recipe ... Ciao, Bjoern Hi, I have GATK 2.4 running in our local galaxy, next to the default galaxy 1.x version. Both are in the tool menu, but only users that have provided a licence or proof that they are from an academic site have access to the 2.4 version. This is based on a usergroup check in a dynamic job runner configuration. I used modified the GATK 2 tool configuration from the test toolshed (by jjohnson). Modifications to the xmls included: --max_jvm_heap xG instead of --max_jvm_heap_fraction 1 : we use shared nodes, so it's not allowed to use all ram. --num_threads : some hard coded thread settings were changed made sure the '--et 'NO_ET' is commented out, as we don't have a key. relevant dynamic_runner part: from galaxy.jobs.mapper import JobMappingException if 'gatk2' in tool_id = 0: user_group_assocs = user.groups or [] user_has_license = 'gatk2_license' in [user_group_assoc.group.name for user_group_assoc in user_group_assocs] if not user_has_license: raise JobMappingException(GATKv2 is only available to non-profit, academic users. Please send a mail to geert.vandewey...@uantwerpen.be to confirm this.) Best, Geert On 11/19/2013 12:26 PM, Bjoern Gruening wrote: Hi, I found that the GATK tools do not have the same requirement tag. For example indel-realigner has version 1.4, realigner_target_creator has version 1.3. Is that correct? What is the recent version that is required for GATK? Also realigner_target_creator uses the gatk_picard_indexes location file, but under tool-data is only a gatk_sorted_picard_indexes.loc file. Are there any concrete plans for the GATK wrappers. Especially to update to a newer version. Or is that not feasible because of this complicated license policy and the phone-home option ... I found the following trello card, but its a little bit outdated: https://trello.com/c/IPkT2spd Is anyone running a recent GATK version in Galaxy? Thanks! Bjoern ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] secure Galaxy with SSL
Hi Nate,
Thanks so much for the help.
Aslo, I solved my second issue. Here are the the changes I made to the Apache
conf file.
RewriteCond %{HTTPS} off
#RewriteRule ^(.*) http://localhost:8080$1 [P]
RewriteRule ^/?(.*) https://%{SERVER_NAME}/$1 [R,L]
Now http will be redirected to https. Just put it here for future reference in
case anyone needs to know.
Best,
Jim
From: Nate Coraor n...@bx.psu.edu
Sent: Tuesday, November 19, 2013 1:14 PM
To: Jingchao Zhang
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] secure Galaxy with SSL
On Tue, Nov 19, 2013 at 12:32 PM, Jingchao Zhang
zh...@unl.edumailto:zh...@unl.edu wrote:
Hi Peter,
Thanks so much for your help! It is like you said a browser issue.
I also noticed that the Galaxy main server (https://usegalaxy.org/) doesn't
have this problem. And their USCS main table browser uses https instead of
http. Does anyone know why this isn't included in the current Galaxy release?
And how can I change my current http USCS main to https USCS main?
Hi Jim,
We did this for usegalaxy.orghttp://usegalaxy.org simply by locally changing
the URL in the tool's config from http to https. A proper fix for this tool
(and other external sites which open in the center iframe) is in the works and
will be released to the stable branch once it's done.
--nate
Thanks,
Jim
Message: 8
Date: Tue, 19 Nov 2013 08:51:03 +
From: Peter Briggs
peter.bri...@manchester.ac.ukmailto:peter.bri...@manchester.ac.uk
To: galaxy-dev@lists.bx.psu.edumailto:galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] secure Galaxy with SSL
Message-ID:
528b2677.9050...@manchester.ac.ukmailto:528b2677.9050...@manchester.ac.uk
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hello Jim
Re your problem #1 (UCSC browser appears to be blocked), I've seen
something similar with our local Galaxy instance, which is also served
via https.
In our case I believe this is actually a browser issue: the latest
version of Firefox silently blocks mixed secure and insecure content:
https://blog.mozilla.org/tanvi/2013/04/10/mixed-content-blocking-enabled-in-firefox-23/
(I think Chrome and IE do something similar, although IE at least gives
a warning.)
The workaround is either to disable mixed content blocking (not trivial
in Firefox, and probably not a good idea in general), or to do something
like e.g. right-click Open link in new tab on the Get data/UCSC
main table browser link in Galaxy.
Once UCSC has loaded in the new tab it can be used to send data back to
Galaxy without any problems.
HTH
Best wishes, Peter
On 18/11/13 23:03, Jingchao Zhang wrote:
Dear all,
Today I installed the SSL module for our local Galaxy instance and the
https://; link is working fine. I added this
Location/
RequestHeader set X-URL-SCHEME https
/Location
in our Apache configuration file as instructed in this webpage:
http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy
Here are my problems with SSL:
1. Some build in links like UCSC Main
http://genome.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=https%3A//hcc-galaxy.unl.edu/tool_runnertool_id=ucsc_table_direct1hgta_compressType=nonesendToGalaxy=1hgta_outputType=bed
table
browser and UCSC Test
http://genome-test.cse.ucsc.edu/cgi-bin/hgTables?GALAXY_URL=https%3A//hcc-galaxy.unl.edu/tool_runnertool_id=ucsc_table_direct_test1hgta_compressType=nonesendToGalaxy=1hgta_outputType=bed
table
browser become invalid. If I click on them, nothing will happen, as if
they are blocked.
2. The old http link still works, which I think shouldn't because I
added the RequestHeader ... https line in Apache configuration. I
really want to disable the http link because the new users could be
easily led to the old one.
Both httpd and Galaxy have been restarted after the changes are made.
Since I didn't find any similar threads in the mailist, I hope someone
here can help me out with this.
Thanks,
Jim
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--
Peter Briggs peter.bri...@manchester.ac.ukmailto:peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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[galaxy-dev] Local installation problem
Hi there,
I am trying to install Galaxy locally on my Mac OSX 10.9, python 2.7.
Nonetheless, when I run it, it says that some eggs are out of date. I have
fetched them, but the following message appears:
Mac-Pro-Cesar-Rodriguez:scripts Rodriguez$ python fetch_eggs.py
Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Warning: pycrypto (a dependent egg of Fabric) cannot be fetched
Fetched http://eggs.galaxyproject.org/paramiko/paramiko-1.11.1-py2.7.egg
One of Galaxy's managed eggs depends on something which is missing, this is
almost certainly a bug in the egg distribution.
Dependency paramiko requires pycrypto=2.1,!=2.4
Traceback (most recent call last):
File fetch_eggs.py, line 37, in module
c.resolve() # Only fetch eggs required by the config
File /Users/Rodriguez/galaxy-dist/lib/galaxy/eggs/__init__.py, line 345,
in resolve
egg.resolve()
File /Users/Rodriguez/galaxy-dist/lib/galaxy/eggs/__init__.py, line 168,
in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File /Users/Rodriguez/galaxy-dist/lib/pkg_resources.py, line 569, in
resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (paramiko 1.11.1
(/Users/Rodriguez/galaxy-dist/eggs/paramiko-1.11.1-py2.7.egg),
Requirement.parse('pycrypto=2.1,!=2.4¹))
What should I do to fix this?
Thank you so much for your help.
Cesar
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Re: [galaxy-dev] unable to share dataset history
Hi, That sort of sharing only works within a single galaxy instance; users are not shared between different galaxies. To copy an entire history from one instance to another you will want to use the history export/import functionality. History context menu - Export to file on the source instance, and Import from file on the destination. -Dannon On Tue, Nov 19, 2013 at 11:20 AM, Manisha Sapre msa...@nmdp.org wrote: Hello Team Galaxy trying to share/ forward dataset history from user 1 ( running on a local instance,Scrn.1) to user 2 (running on cloud amazon ec2 instance,Scrn.2) and *vice-versa*, error:- user is not a valid galaxy user. getting this error while both the users are logged into system and both the instance's are running normal. insights of team will be very helpful. Thanks msapre ___ 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/
