- galaxy-dev - lists.galaxyproject.org

Fwd: Seeking Help with Galaxy
by Anton Nekrutenko 16 Oct '15

16 Oct '15

Tendai: I'm forwarding your e-mail to the dev forum. This is the best place to ask these kinds of questions. a. ---------- Forwarded message ---------- From: Mutangadura, Tendai <tendai(a)missouri.edu> Date: Thu, Oct 15, 2015 at 7:17 PM Subject: Seeking Help with Galaxy To: "anton(a)bx.psu.edu" <anton(a)bx.psu.edu> Cc: "Mutangadura, Tendai" <tendai(a)missouri.edu> Dr. Nekrutenko, I have been trying to learn how to use Galaxy using the Galaxy Main Server for some time but I have just convinced my boss to allow me to convert a computer that was laying idle as a Linux machine and I am planning to install my local instance of Galaxy there. I have been watching some of your Vimeo instructional videos on using Galaxy and I wanted to find out if I could from time to ask you or your mentees questions as I try to set up my Galaxy instance. My first question is this: is there a difference between downloading and installing tools to the cloud and doing the same installation on my Linux desktop? (I downloaded 2 of your videos yesterday on doing this on the cloud). My Linux computer has Centos7 installed on it, has 500GB storage and 8GB RAM. I also have 5 a TB external hard drive that I can use in conjunction with the desktop. Can I accomplish much more with this compared to what I can do on my main server Galaxy account? The main focus of our lab is the use of whole genome sequencing (WGS) to discover disease causing mutations in dogs, and our lab has made several discoveries this way. Like many reference genomes, the dog genome reference has quite a few gaps. My immediate aim after installing my local instance of Galaxy is to use a 88200 bp bac sequence that bridges a gap in the dog reference that our collaborators made available to us (they filled the gap by Sanger Sequencing/chromosome walking) and use this as the reference sequence to align against reads from various dogs that we have whole genome sequences for. If you have the time, could you please give me some guidance as to the best way to do this? The bac sequence is already in fasta format. I have access to WGS files of raw sequence reads in the original, unprocessed state as in the form in which the reads came off the Illumina sequencing machine, and also in versions subsequent to our bionformatician’s quality control manipulation and error correction (using MaSuRCA. My plan is to start practicing (before my local Galaxy is up and running) by 1. Uploading the bac sequence and use this as my ‘reference” 2. Upload all the paired reads for one dog 3. Align the paired reads using appropriate software (BWA?) 4. Call Variants using Freebayes? 5. Do this for several dogs and compare the VCF of the various dogs 6. Hope to identify disease-causing variants that we potentially missed due to no alignment because the reads have no sequence to align to. 7. After this I hope to come up with a workflow which I can save and export to my local Galaxy. (I already have the above sequences uploaded into my Galaxy main server account). Thank you for your time and for posting the instructional videos that I have already learnt so much from. Tendai Mutangadura (I publish papers as Tendai Mhlanga-Mutangadura) -- Anton Nekrutenko Professor of Biochemistry and Molecular Biology *http://nekrut.bx.psu.edu <http://nekrut.bx.psu.edu>* (814) 826-3051

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CloudMan launch error
by Aaron Darling 16 Oct '15

16 Oct '15

Hi all, I'm new to CloudMan, and trying to launch a cluster via GVL (3 or 4) on NeCTAR. I'm able to get a head node running without trouble via launch.genome.edu.au, but launching worker nodes from the CloudMan interface appears to fail. CloudMan reboots the worker repeatedly before giving up. I logged into the worker to inspect log files and found the following, but it's not obvious to me what to do next. Hope this is something simple? ubuntu@server-fbbd9a10-fb58-48d8-89cd-5ddd22821648:~$ cat /mnt/cm/paster.log Python version: (2, 7) Image configuration suports: {'apps': ['cloudman', 'galaxy']} 2015-10-15 14:15:24,973 DEBUG app:73 Initializing app 2015-10-15 14:15:24,973 DEBUG ec2:109 Gathering instance zone, attempt 0 2015-10-15 14:15:25,140 DEBUG ec2:115 Instance zone is 'NCI' 2015-10-15 14:15:25,140 DEBUG ec2:44 Gathering instance ami, attempt 0 2015-10-15 14:15:25,459 DEBUG app:76 Running on 'openstack' type of cloud in zone 'NCI' using image 'ami-00003484'. 2015-10-15 14:15:25,459 DEBUG app:98 Getting pd.yaml 2015-10-15 14:15:25,459 DEBUG openstack:99 Establishing a boto Swift connection. 2015-10-15 14:15:25,459 DEBUG openstack:109 Got boto Swift connection. 2015-10-15 14:15:26,112 DEBUG misc:578 Retrieved file 'persistent_data.yaml' from bucket 'cm-45b53bf5024e962bd27e15fd81fcc07d' on host 'swift.rc.nectar.org.au' to 'pd.yaml'. 2015-10-15 14:15:26,118 INFO app:119 Worker starting 2015-10-15 14:15:26,136 DEBUG ec2:76 Gathering instance id, attempt 0 2015-10-15 14:15:26,338 DEBUG ec2:82 Instance ID is 'i-0019a2fc' 2015-10-15 14:16:29,488 DEBUG comm:134 AMQP Connection Failure: [Errno 110] Connection timed out 2015-10-15 14:16:29,492 DEBUG base:57 Enabling 'root' controller, class: CM 2015-10-15 14:16:29,494 DEBUG buildapp:93 Enabling 'httpexceptions' middleware 2015-10-15 14:16:29,496 DEBUG buildapp:99 Enabling 'recursive' middleware 2015-10-15 14:16:29,499 DEBUG buildapp:119 Enabling 'print debug' middleware 2015-10-15 14:16:29,506 DEBUG buildapp:133 Enabling 'error' middleware 2015-10-15 14:16:29,507 DEBUG buildapp:143 Enabling 'config' middleware 2015-10-15 14:16:29,508 DEBUG buildapp:147 Enabling 'x-forwarded-host' middleware 2015-10-15 14:16:29,517 DEBUG misc:768 'cp /etc/hosts /etc/hosts.orig' command OK 2015-10-15 14:16:29,528 DEBUG misc:768 'cp /tmp/tmpuV3NTJ /etc/hosts' command OK Starting server in PID 2825. 2015-10-15 14:16:29,533 DEBUG misc:768 'chmod 644 /etc/hosts' command OK 2015-10-15 14:16:29,533 DEBUG worker:558 Trying to setup AMQP connection; conn = '<cm.util.comm.CMWorkerComm object at 0x2743950>' serving on 0.0.0.0:42284 view at http://127.0.0.1:42284 2015-10-15 14:17:32,656 DEBUG comm:134 AMQP Connection Failure: [Errno 110] Connection timed out 2015-10-15 14:17:32,656 DEBUG worker:558 Trying to setup AMQP connection; conn = '<cm.util.comm.CMWorkerComm object at 0x2743950>' 2015-10-15 14:18:35,760 DEBUG comm:134 AMQP Connection Failure: [Errno 110] Connection timed out 2015-10-15 14:18:35,760 DEBUG worker:558 Trying to setup AMQP connection; conn = '<cm.util.comm.CMWorkerComm object at 0x2743950>' 2015-10-15 14:19:38,864 DEBUG comm:134 AMQP Connection Failure: [Errno 110] Connection timed out 2015-10-15 14:19:38,864 DEBUG worker:558 Trying to setup AMQP connection; conn = '<cm.util.comm.CMWorkerComm object at 0x2743950>' ubuntu@server-fbbd9a10-fb58-48d8-89cd-5ddd22821648:~$ cat /tmp/cm/cm_boot.py.log 2015-10-15 14:23:43,713 DEBUG cm_boot:430 - virtual-burrito seems to be installed 2015-10-15 14:23:44,037 DEBUG cm_boot:25 - Successfully ran '/bin/bash -l -c 'VIRTUALENVWRAPPER_LOG_DIR=/tmp/; HOME=/home/ubuntu; . /home/ubuntu/.venvburrito/startup.sh; lsvirtualenv | grep CM'' 2015-10-15 14:23:44,037 DEBUG cm_boot:433 - 'CM' virtualenv found 2015-10-15 14:23:44,049 DEBUG cm_boot:493 - Fixing /etc/hosts on NeCTAR 2015-10-15 14:23:44,930 INFO cm_boot:244 - << Starting nginx >> 2015-10-15 14:23:44,931 DEBUG cm_boot:169 - Reconfiguring nginx conf 2015-10-15 14:23:44,931 INFO cm_boot:286 - Attempting to configure max_client_body_size in /usr/nginx/conf/nginx.conf 2015-10-15 14:23:44,934 DEBUG cm_boot:25 - Successfully ran 'cp /usr/nginx/conf/nginx.conf /tmp/cm/original_nginx.conf' 2015-10-15 14:23:44,936 DEBUG cm_boot:25 - Successfully ran 'uniq /tmp/cm/original_nginx.conf > /usr/nginx/conf/nginx.conf' 2015-10-15 14:23:44,937 DEBUG cm_boot:25 - Successfully ran 'grep 'client_max_body_size' /usr/nginx/conf/nginx.conf' 2015-10-15 14:23:44,938 DEBUG cm_boot:265 - Creating tmp dir for nginx /mnt/galaxy/upload_store 2015-10-15 14:23:44,938 DEBUG cm_boot:68 - Checking /usr/local/sbin/nginx 2015-10-15 14:23:44,938 DEBUG cm_boot:58 - /usr/local/sbin/nginx is file: False; it's executable: False 2015-10-15 14:23:44,938 DEBUG cm_boot:68 - Checking /usr/local/bin/nginx 2015-10-15 14:23:44,938 DEBUG cm_boot:58 - /usr/local/bin/nginx is file: False; it's executable: False 2015-10-15 14:23:44,938 DEBUG cm_boot:68 - Checking /usr/bin/nginx 2015-10-15 14:23:44,938 DEBUG cm_boot:58 - /usr/bin/nginx is file: False; it's executable: False 2015-10-15 14:23:44,938 DEBUG cm_boot:68 - Checking /usr/sbin/nginx 2015-10-15 14:23:44,938 DEBUG cm_boot:58 - /usr/sbin/nginx is file: False; it's executable: False 2015-10-15 14:23:44,938 DEBUG cm_boot:68 - Checking /sbin/nginx 2015-10-15 14:23:44,939 DEBUG cm_boot:58 - /sbin/nginx is file: False; it's executable: False 2015-10-15 14:23:44,939 DEBUG cm_boot:68 - Checking /bin/nginx 2015-10-15 14:23:44,939 DEBUG cm_boot:58 - /bin/nginx is file: False; it's executable: False 2015-10-15 14:23:44,939 DEBUG cm_boot:68 - Checking /usr/sbin/nginx 2015-10-15 14:23:44,939 DEBUG cm_boot:58 - /usr/sbin/nginx is file: False; it's executable: False 2015-10-15 14:23:44,939 DEBUG cm_boot:68 - Checking /usr/nginx/sbin/nginx 2015-10-15 14:23:44,939 DEBUG cm_boot:58 - /usr/nginx/sbin/nginx is file: True; it's executable: True 2015-10-15 14:23:44,939 DEBUG cm_boot:270 - Using '/usr/nginx/sbin/nginx' as the nginx executable 2015-10-15 14:23:44,946 ERROR cm_boot:31 - Error running 'ps xa | grep nginx | grep -v grep'. Process returned code '1' and following stderr: '' 2015-10-15 14:23:44,964 DEBUG cm_boot:25 - Successfully ran '/usr/nginx/sbin/nginx' 2015-10-15 14:23:44,966 DEBUG cm_boot:25 - Successfully ran 'rm -rf /mnt/galaxy/upload_store' 2015-10-15 14:23:44,966 DEBUG cm_boot:281 - Deleting tmp dir for nginx /mnt/galaxy/upload_store 2015-10-15 14:23:44,966 INFO cm_boot:339 - << Downloading CloudMan >> 2015-10-15 14:23:44,966 DEBUG cm_boot:43 - Checking existence of directory '/mnt/cm' 2015-10-15 14:23:44,966 DEBUG cm_boot:52 - Directory '/mnt/cm' exists. 2015-10-15 14:23:44,966 DEBUG cm_boot:344 - Using user-provided default bucket: cloudman-gvl-304 2015-10-15 14:23:44,966 INFO cm_boot:324 - Connecting to a custom Object Store 2015-10-15 14:23:44,967 DEBUG cm_boot:333 - Got boto S3 connection: S3Connection:swift.rc.nectar.org.au 2015-10-15 14:23:44,967 DEBUG cm_boot:210 - Checking if key 'cm.tar.gz' exists in bucket 'cm-45b53bf5024e962bd27e15fd81fcc07d' 2015-10-15 14:23:45,276 INFO cm_boot:356 - CloudMan found in cluster bucket 'cm-45b53bf5024e962bd27e15fd81fcc07d'. 2015-10-15 14:23:45,276 DEBUG cm_boot:190 - Getting file cm.tar.gz from bucket cm-45b53bf5024e962bd27e15fd81fcc07d 2015-10-15 14:23:45,276 DEBUG cm_boot:194 - Attempting to retrieve file 'cm.tar.gz' from bucket 'cm-45b53bf5024e962bd27e15fd81fcc07d' 2015-10-15 14:23:45,726 INFO cm_boot:197 - Successfully retrieved file 'cm.tar.gz' from bucket 'cm-45b53bf5024e962bd27e15fd81fcc07d' via connection 'swift.rc.nectar.org.au' to '/mnt/cm/cm.tar.gz' 2015-10-15 14:23:45,727 DEBUG cm_boot:388 - Getting metadata 'revision' for file 'cm.tar.gz' from bucket 'cm-45b53bf5024e962bd27e15fd81fcc07d' -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email.

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Galaxy Interactive Environment devs
by Eric Rasche 15 Oct '15

15 Oct '15

Howdy y'all, I'm building some changes to the IE infrastructure that will fix some initial hacks we did, however they will be backwards incompatible. Specifically these changes will fix some of the enterprise deployment pains (running with an external upstream proxy like apache) and allow for safely running IEs on a separate host. I'm emailing the dev list to see if anyone else has started building IEs, or if it just Björn and myself. Feel free to make yourselves known to us so we know who to contact when we're planning new features :) If you're just building on top of our existing containers, this won't be an issue for you, you'll just need to rebuild your containers once we release 15.10 versions. Cheers, Eric -- Eric Rasche Programmer II Center for Phage Technology Rm 312A, BioBio Texas A&M University College Station, TX 77843 404-692-2048 esr(a)tamu.edu

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CORS requests to public Galaxy server
by Marco Ocana 15 Oct '15

15 Oct '15

Hi, I am attempting to access the public usegalaxy.org server using the REST API from web browsers. The question: I am not seeing Access-Control-Allow-* headers in REST API responses. Are browser REST CORS requests supported by the Galaxy servers? More details: Here is an error reported by Chrome during a preflight OPTIONS request for a GET https://usegalaxy.org/api/tools?key=MYREALKEY request. XMLHttpRequest cannot load https://usegalaxy.org/api/tools?key=xxxxxx. No 'Access-Control-Allow-Origin' header is present on the requested resource. Origin 'http://localhost:63342' is therefore not allowed access. The response had HTTP status code 404. The request headers: 1. Accept: */* 2. Accept-Encoding: gzip, deflate, sdch 3. Accept-Language: en-US,en;q=0.8,es;q=0.6 4. Access-Control-Request-Headers: accept, content-type, gs-toolname 5. Access-Control-Request-Method: GET 6. Connection: keep-alive 7. Host: usegalaxy.org 8. Origin: http://localhost:63342 9. Referer: http://localhost:63342/GSRemoteComputatio/TestWidgetsWithRemoteJobs.html 10. User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/45.0.2454.101 Safari/537.36 The response headers from Galaxy: 1. Connection: keep-alive 2. Content-Encoding: gzip 3. Content-Type: text/html 4. Date: Tue, 13 Oct 2015 22:14:31 GMT 5. Server: nginx/1.4.7 6. Transfer-Encoding: chunked 7. Vary: Accept-Encoding Thanks Marco

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Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)
by Daniel Blankenberg 15 Oct '15

15 Oct '15

Hi Lance, I looked at this a bit ago and had similar concerns, particularly with the outputs and inputs not being well-defined. In addition to the output tar ball —> local, extract —> upload not being great, as you mention, the input datatypes, etc, could use some work — in the very least, we should definitely create a nice biom datatype and have some converters available (import and export). Definitely worth spending some extra time to make sure that we have the data flowing well between each of the different parts/tools, and even better to make sure that its done in a way that allows mixing and matching with other non-qiime tools. One thing that we want to avoid is large amounts of manual massaging of the automatically generated xml; fixing things up once might not be too bad, but having to do it with each new tool version can be “frustrating". Although perhaps having a good starting point and only needing to manually modify for any updates could be good enough (I’m not very familiar with the extent of typical changes between qiime versions to make a call on how much changes). Dan (resending since I received a message bounce from list) On Oct 6, 2015, at 9:59 AM, Daniel Blankenberg <dan(a)bx.psu.edu> wrote: > Hi Lance, > > I looked at this a bit ago and had similar concerns, particularly with the outputs and inputs not being well-defined. In addition to the output tar ball —> local, extract —> upload not being great, as you mention, the input datatypes, etc, could use some work — in the very least, we should definitely create a nice biom datatype and have some converters available (import and export). > > Definitely worth spending some extra time to make sure that we have the data flowing well between each of the different parts/tools, and even better to make sure that its done in a way that allows mixing and matching with other non-qiime tools. > > > One thing that we want to avoid is large amounts of manual massaging of the automatically generated xml; fixing things up once might not be too bad, but having to do it with each new tool version can be “frustrating". Although perhaps having a good starting point and only needing to manually modify for any updates could be good enough (I’m not very familiar with the extent of typical changes between qiime versions to make a call on how much changes). > > > > > Dan > > > On Oct 5, 2015, at 5:26 PM, Lance Parsons <lparsons(a)princeton.edu> wrote: > >> I was recently asked if I could provide a QIIME analysis pipeline for 16S data in Galaxy using tools in the QIIME pipeline (http://qiime.org/) >> >> I did a bit of looking around for existing Galaxy wrappers and found an application that generates the wrappers for QIIME scripts for Galaxy (https://github.com/qiime/qiime-galaxy) This is a very well written application that does a great job of wrapping the QIIME scripts for Galaxy. However, there are a few things about it that don't quite fit my needs. >> >> 1. The tools output tgz files of all of the output files. This means that to execute a pipeline, the user would have to download the tgz files, untar, and then upload whichever file(s) are needed for the next step. >> 2. There is no toolshed repository to install the dependencies for these tools, making it a tricky for administrators to automate and also maintain various versions of QIIME going forward. >> 3. There are no toolshed versions of the tools themselves, which also makes installation and integration a bit tricky and makes it hard to me to create and manage updates, fixes, tweaks, etc. There are also no tests, etc. >> >> For these reasons I decided to investigate the feasibility of using the generated wrappers as a basis for a "toolshed" version of QIIME. If anyone is interested in helping, or has suggestions, or is working on something related, I'd be very happy to collaborate. >> >> The repository for the WIP is at https://github.com/lparsons/galaxy_tools/tree/qiime/tools/qiime1.9.0. There is also a package on the testtoolshed as well as a first pass at package_qiime_1_9_1 (https://github.com/lparsons/galaxy_tools/tree/qiime/packages/package_qiime_…) >> >> -- >> Lance Parsons - Scientific Programmer >> 134 Carl C. Icahn Laboratory >> Lewis-Sigler Institute for Integrative Genomics >> Princeton University >> >> ___________________________________________________________ >> 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: >> https://lists.galaxyproject.org/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ >

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galaxy / sartools / bug
by Sabrina Legoueix Rodriguez 15 Oct '15

15 Oct '15

Dear Sir, Madam, I am working on the integration of sartools_1_1_0 in our local galaxy instance. This tool can be found at: http://toolshed.france-bioinformatique.fr/repository When we use deseq2 from this package, the temporary working directory located in the "job_working_directory" seems to be deleted too early, and so the "rsync" commands from "abims_sartools_deseq2_wrapper.py" script can't be executed because the files do not exist anymore. Here is the error message: rsync: change_dir "/work/galaxy-dev/database/job_working_directory/038/38633/figures" failed: No such file or directory (2) rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1039) [sender=3.0.6] rsync: change_dir "/work/galaxy-dev/database/job_working_directory/038/38633/tables" failed: No such file or directory (2) rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1039) [sender=3.0.6] rsync: link_stat "/work/galaxy-dev/database/job_working_directory/038/38633/Project.RData" failed: No such file or directory (2) rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1039) [sender=3.0.6] rsync: link_stat "/work/galaxy-dev/database/job_working_directory/038/38633/Project_report.html" failed: No such file or directory (2) rsync error: some files/attrs were not transferred (see previous errors) (code 23) at main.c(1039) [sender=3.0.6] Could you please help us on this problem? Thank you very much in advance. Best regards, Sabrina **Sabrina LEGOUEIX RODRIGUEZ** Responsable Plateau Bioinformatique Tél. : +33 (0) 5 61 28 57 92 sabrina.legoueix(a)toulouse.inra.fr <mailto:[MAIL]> www.toulouse-white-biotechnology.com <http://www.toulouse-white-biotechnology.com/> LinkedIn <https://www.linkedin.com/company/2757525h> Twitter <https://twitter.com/TWB_Biotech> TWB - Parc technologique du canal • Bâtiment NAPA CENTER B • 3, rue Ariane • 31520 Ramonville Saint-Agne Ce message et ses pièces jointes sont strictement personnels. Ils peuvent contenir des informations confidentielles. Si vous avez reçu ce message par erreur, merci d'en avertir l'expéditeur et de détruire le message et les documents joints. Toute utilisation des informations reçues par erreur est interdite. This message and the attachments are strictly personal. They may contain confidential information. If you have received this message in error, please notify the sender and delete the message and the attachments. Any use of this communication received in error is prohibited.

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tomorrow's GalaxyAdmins Online Meetup: Galaxy at Analome with David Kovalic
by Hans-Rudolf Hotz 14 Oct '15

14 Oct '15

Hi all this is just a reminder about our next GalaxyAdmins Online Meetup: The October meetup will be tomorrow at 5pm Central European Summer Time see: https://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2015_10_15 (there you will find the "Meeting Room Link" and your "local time") The main presentation will be by David Kovalic, Analome Inc. Galaxy at Analome – Outreach, Opportunity and Challenges At Analome Galaxy has found another home and we like it for numerous reasons. In this talk we will present the multifaceted role Galaxy plays at Analome and how it supports ongoing bioinformatics projects while at the same time providing opportunities for social good. Second, we gonna have "News from the Galaxy project": Galaxy Wiki Replacement: Options, thoughts, and questions I hope many of you will join us Dave and Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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Re: [galaxy-dev] pbs_python can't be installed via scramble
by Makis Ladoukakis 14 Oct '15

14 Oct '15

Hello Will, The second command returns the container.hpp inside the directory of the torque source which i used to install it: find / -name container.hpp /home/user/torque-5.1.1.2-1_18e4a5f1/src/include/container.hpp I noticed there is also a log.h file there. the first command doesn't return anything (I've search manually too, nothing inside /usr/local/include/). How do I fix this? Shall I change the export command of PBS_PYTHON_INCLUDEDIR? Thank you, Makis Date: Thu, 24 Sep 2015 08:31:07 -0700 Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble From: wholtz(a)lygos.com To: makis4ever(a)hotmail.com CC: galaxy-dev(a)lists.galaxyproject.org And does find /usr/local/include -name container.hppor find / -name container.hppreturn torque/src/include/container.hpp ? My guess is you installed binaries for Torque, but the scrambling requires the Torque source (or at least the header files form Torque). -Will On Thu, Sep 24, 2015 at 1:16 AM, Makis Ladoukakis <makis4ever(a)hotmail.com> wrote: Hello Will, Thanks again for your reply. Yes I had already tried these but I got the same container.hpp error. The only thing different in my case is that the names of the directories of the directories are a bit different: export PBS_PYTHON_INCLUDEDIR=/usr/local/include/ export PBSCONFIG=/usr/local/bin/pbs-config export LIBTORQUE_DIR=/usr/local/lib/libtorque.so python scripts/scramble.py -e pbs_python Any ideas? Kind regards, Makis Date: Wed, 23 Sep 2015 07:06:32 -0700 Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble From: wholtz(a)lygos.com To: makis4ever(a)hotmail.com CC: galaxy-dev(a)lists.galaxyproject.org Hi Makis, The thread I posted does have the exact same container.hpp error and proposes a solution. Did you try setting your PBS_PYTHON_INCLUDEDIR to point to your torque/include directory, as mentioned in that thread? from the thread:export PBS_PYTHON_INCLUDEDIR=/usr/local/torque/include/ export PBSCONFIG=/usr/local/torque/bin/pbs-config export LIBTORQUE_DIR=/usr/local/torque/lib/libtorque.so -Will On Wed, Sep 23, 2015 at 5:49 AM, Makis Ladoukakis <makis4ever(a)hotmail.com> wrote: Hello Will, Thank you for your reply. I had already checked this thread before as I browsed through the mailing list for "pbs_python" issues. It doesn't have the same errors (can't locate log.h and when i provide it it wants the container.hpp ) and up to one point i've already followed the "rescrambling" of the pbs_python. Anyone else had any experience with that? Thank you, Makis Date: Tue, 22 Sep 2015 09:35:11 -0700 Subject: Re: [galaxy-dev] pbs_python can't be installed via scramble From: wholtz(a)lygos.com To: makis4ever(a)hotmail.com CC: galaxy-dev(a)lists.galaxyproject.org Here is an old thread that looks rather similar to your problems:https://www.mail-archive.com/galaxy-dev@lists.galaxyproject.org/ms… -Will On Tue, Sep 22, 2015 at 2:43 AM, Makis Ladoukakis <makis4ever(a)hotmail.com> wrote: Hello everyone, I'm trying to set up a Galaxy instance on a multi-core server in my university so according to the instructions here: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS I installed Torque, changed the eggs.ini file by adding the 4.4.0. version of pbs_python and tried to setup pbs_python via scramble: LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python When I did that I got the error: Failed to find log.h in inlcude dir /usr/include/torque. (Set incude dir via PBS_PYTHON_INCLUDEDIR variable) Traceback (most recent call last): File "scripts/scramble.py", line 50, in <module> egg.scramble() File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 57, in scramble self.run_scramble_script() File "/home/galaxy/galaxy/lib/galaxy/eggs/scramble.py", line 210, in run_scramble_script raise ScrambleFailure( self, "%s(): Egg build failed for %s %s" % ( sys._getframe().f_code.co_name, self.name, self.version ) ) galaxy.eggs.scramble.ScrambleFailure: run_scramble_script(): Egg build failed for pbs_python 4.4.0 so I did some digging around and found that the file I need is in /scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/ (please correct me if I am wrong) So I tried again using: PBS_PYTHON_INCLUDEDIR=/home/galaxy/galaxy/scripts/scramble/build/py2.7-linux-x86_64-ucs4/pbs_python/src/C++/ LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python but then I got the error: In file included from src/C++/pbs_ifl.h:90:0, from src/C++/pbs_wrap.cxx:2978: /usr/local/include/u_hash_map_structs.h:82:25: fatal error: container.hpp: No such file or directory #include "container.hpp" Can someone help me please? Kind regards, Makis ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz(a)lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email. -- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz(a)lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email. -- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at wholtz(a)lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email.

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MS Active Directory Authentication
by McCully, Dwayne (NIH/NIAMS) [C] 14 Oct '15

14 Oct '15

Hello Everyone, Is there an example of the auth_config.xml for a MS Active directory connection? I would like to all my users to register and login to Galaxy with their AD username and password. Note: We don't use a "@example.com" extension for our usernames just "username". Thanks in advance Dwayne

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External User Authenticaion
by Ryan G 13 Oct '15

13 Oct '15

Hi all - I'm trying to use external user authentication with Galaxy. The external authentication passes to Galaxy the username with the mail domain at HTTP_USER. In galaxy.ini, I enable: use_remote_user = True When I try to access Galaxy, I get the message: 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. But nothing in paster.log indicating what the error is. How do I track this down?

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