January 2014 - galaxy-dev - lists.galaxyproject.org

faToTwoBit: not found / trackster
by Jasper Jan Koehorst 04 Jan '14

04 Jan '14

First of all, best wishes! I was/am trying to visualize a GTF file in galaxy on a local 64 bit ubuntu system. However I stumbled upon an issue were it remained grey. When I did an automaic visualization I saw a line that went up and down over the chromosome. When I switched to pack I got a grey / / / line slashed output. I contacted dannon and ceberhard on IRC and they told me to add a print statement on line 200 for the tracker. This visualized the following error: {'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'} So I downloaded and placed the faToTwoBit file in /usr/bin I even chmodded it to 777 but the error remained. I also started digging into the code on where it calls the application and added /usr/bin/ in front of it but no luck so far. Anyone has a clue on what is happening? It almost must be an ubuntu related issue as I dont see how galaxy cannot find the path. $PATH is still properly set when running galaxy as I added echo $path it to a tool and it returned /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/bin The IRC chat can be seen here: http://pastebin.com/9fZrkRDn Thanks a lot, /home/galaxy/HB27.2bit10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=0&high=320487&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" 10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1602432&high=1894876&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" 10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1281945&high=1602432&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" 10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=320486&high=640973&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" 10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=961459&high=1281946&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" 10.64.9.118 - - [03/Jan/2014:17:24:34 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=640972&high=961459&mode=Auto&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 200 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" {'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'} galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:36,418 Error in dataset API at listing contents: 'data': 'data' Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show rval = self._data( trans, dataset, **kwd ) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data ref_seq = data_dict[ 'data' ] KeyError: 'data' 10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=320486&high=640973&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" {'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'} galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:36,595 Error in dataset API at listing contents: 'data': 'data' Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show rval = self._data( trans, dataset, **kwd ) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data ref_seq = data_dict[ 'data' ] KeyError: 'data' 10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=0&high=320487&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" {'kind': 'error', 'message': '/bin/sh: 1: faToTwoBit: not found\n'} {'kind': 'error'galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,049 Error in dataset API at listing contents: 'data': 'data' Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show rval = self._data( trans, dataset, **kwd ) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data ref_seq = data_dict[ 'data' ] KeyError: 'data' , 'message': '/bin/sh: 1: faToTwoBit: not found\n'} 10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1602432&high=1894876&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" {{'kind': 'error', 'message''kind'galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,099 Error in dataset API at listing contents: 'data': 'data' Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show rval = self._data( trans, dataset, **kwd ) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data ref_seq = data_dict[ 'data' ] KeyError: 'data' : : 'error'10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=961459&high=1281946&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" '/bin/sh: 1: faToTwoBit: not found\n', 'message': '/bin/sh: 1: faToTwoBit: not found\n'} } galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,102 Error in dataset API at listing contents: 'data': 'data' Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show rval = self._data( trans, dataset, **kwd ) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data ref_seq = data_dict[ 'data' ] KeyError: 'data' 10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=640972&high=961459&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36" galaxy.webapps.galaxy.api.datasets ERROR 2014-01-03 17:24:37,102 Error in dataset API at listing contents: 'data': 'data' Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 46, in show rval = self._data( trans, dataset, **kwd ) File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/api/datasets.py", line 201, in _data ref_seq = data_dict[ 'data' ] KeyError: 'data' 10.64.9.118 - - [03/Jan/2014:17:24:35 +0200] "GET /api/datasets/e2132aef71b11dbf?data_type=data&chrom=chr&low=1281945&high=1602432&mode=Pack&resolution=801.216067653277&hda_ldda=hda&filter_cols=%5B%22Score%22%5D HTTP/1.1" 500 - " http://ssb4:8082/visualization/trackster?dataset_id=e2132aef71b11dbf&hda_ld…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_1) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/31.0.1650.63 Safari/537.36"

3 2

Can REMOTE_USER be changed to another header variable?
by Jennifer Jackson 03 Jan '14

03 Jan '14

Hello Prakash, I am going to move this over to the galaxy-dev(a)bx.psu.edu mailing list where it will have greater visibility within our development community. Best, Jen Galaxy team https://wiki.galaxyproject.org/MailingLists#The_lists On 1/2/14 7:27 AM, Velayutham, Prakash (Prakash) wrote: > Hi, > > We have a SSO environment provided by Oracle Fusion products and for > some reason, they don't like to send over HTTP_REMOTE_USER as a header > variable to downstream servers. I have seen it before with other web > sites I have integrated with Oracle Access Manager. Is there a way > Galaxy can accept another HEADER variable than REMOTE_USER for its > external authentication? > > As an extension: > > * With just enabling HTTP_REMOTE_USER as a header variable from an > external authenticator, Galaxy works without any issues. I tried > this with a default Apache/mod_ldap/mod_authnz_ldap setup. > * However, when I mix the Oracle gateways into the mix, things break > down. > o I made OAM send HTTP_AUTH_USER over to Galaxy. > o I changed all instances of REMOTE_USER to AUTH_USER in the > installed location of Galaxy in my server. > o Authentication works fine, but I get issues with HISTORY part > of Galaxy (below), when I access a workflow or basically any > part of Galaxy that depends on HISTORY > > > Error Traceback: > > View as: Interactive > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> | > Text > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> | > XML > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > (full) > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > ? |AttributeError: 'NoneType' object has no attribute 'user'| > URL: > http://xxx.xxx.xxx/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-d… > Module weberror.evalexception.middleware:*364* in |respond| > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > view > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > |>> > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…>app_iter > *=* self*.*application*(*environ*,* detect_start_response*)*| > Module paste.recursive:*84* in |__call__| > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > view > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > |>> > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…>*return* > self*.*application*(*environ*,* start_response*)*| > Module galaxy.web.framework.middleware.remoteuser:*91* in |__call__| > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > view > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > |>> > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…>*return* > self*.*app*(* environ*,* start_response *)*| > Module paste.httpexceptions:*633* in |__call__| > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > view > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > |>> > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…>*return* > self*.*application*(*environ*,* start_response*)*| > Module galaxy.web.framework.base:*132* in |__call__| > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > view > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > |>> > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…>*return* > self*.*handle_request*(* environ*,* start_response *)*| > Module galaxy.web.framework.base:*190* in |handle_request| > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > view > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > |>> > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…>body > *=* method*(* trans*,* ****kwargs *)*| > Module galaxy.web.framework:*98* in |decorator| > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > view > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > |>> > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…>*return* > func*(* self*,* trans*,* ***args*,* ****kwargs *)*| > Module galaxy.webapps.galaxy.controllers.dataset:*555* in |list| > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > view > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > |>> > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…>status*,* > message *=* self*.*_copy_datasets*(* trans*,* hda_ids*,* > target_histories *)*| > Module galaxy.webapps.galaxy.controllers.dataset:*1127* in > |_copy_datasets| > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > view > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> > |>> > <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…>*if* > user *!=* history*.*user*:*| > *AttributeError: 'NoneType' object has no attribute 'user'* > > Thanks, > Prakash > > > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org

4 9

an REMOTE_USER be changed to another header variable
by Velayutham, Prakash (Prakash) 03 Jan '14

03 Jan '14

Hi, We have a SSO environment provided by Oracle Fusion products and for some reason, they don't like to send over HTTP_REMOTE_USER as a header variable to downstream servers. I have seen it before with other web sites I have integrated with Oracle Access Manager. Is there a way Galaxy can accept another HEADER variable than REMOTE_USER for its external authentication? As an extension: With just enabling HTTP_REMOTE_USER as a header variable from an external authenticator, Galaxy works without any issues. I tried this with a default Apache/mod_ldap/mod_authnz_ldap setup. However, when I mix the Oracle gateways into the mix, things break down. I made OAM send HTTP_AUTH_USER over to Galaxy. I changed all instances of REMOTE_USER to AUTH_USER in the installed location of Galaxy in my server. Authentication works fine, but I get issues with HISTORY part of Galaxy (below), when I access a workflow or basically any part of Galaxy that depends on HISTORY Error Traceback: View as: Interactive | Text | XML (full) AttributeError: 'NoneType' object has no attribute 'user' URL: http://xxx.xxx.xxx/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-d… Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:91 in __call__ view >> return self.app( environ, start_response ) Module paste.httpexceptions:633 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request view >> body = method( trans, **kwargs ) Module galaxy.web.framework:98 in decorator view >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.dataset:555 in list view >> status, message = self._copy_datasets( trans, hda_ids, target_histories ) Module galaxy.webapps.galaxy.controllers.dataset:1127 in _copy_datasets view >> if user != history.user: AttributeError: 'NoneType' object has no attribute 'user' Thanks, Prakash.

2 2

Is there a way yet to more easily determine name of inputs for renaming in workflows
by Thon deBoer 03 Jan '14

03 Jan '14

Hi, In order to make Galaxy workflows even more useful, it is going to be important for data files to be renamed in a workflow. I know we can use the "#{input1 | base name}-BWA.sam" trick which is useful IF you know what the actual parameter name is in the XML file. There was some discussions some years ago (http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-September/011288.html) but it is is now very time consuming to figure out from the XML file what the name of the input parameter is you would like to use (and it is often very tricky, due to the fact that the name of the actual input parameter may actually change based on some selection in the UI…. I often had to resort to actually chaining the XML file to make the output something like: <data format="sam" name="output" label="#echo os.path.splitext ( str ( $paired.input1.name ).replace ( '_R1' , '' )) [ 0 ]#-bwa_#echo str ( $paired.sPaired ) #.sam”> But that is time consuming and does no longer work with the toolshed since an update of a tool is merely a brute force replacement of the previous version, no longer allowing me to have to change it once and let the updates work with on the changed version as was working brilliantly before all tools were moved out of the main branch and into the toolshed)… So, are there any plans to at least expose the Inputs (or the XML) during the workflow editing or something similar? Now I have to dig up the XML file every time I use a new tool, making the creation of workflow a tedious task... Regards, Thon [cid:enz_logo_2_newf03327] Thon deBoer Director of Software 3415 Colorado Ave. Room A255 Boulder, CO 80303 Cell: (650) 799-6839 tdeboer(a)enzymatics.com www.enzymatics.com Enzymatics Inc. Confidentiality Notice: This e-mail and any attachments are confidential, proprietary and or privileged information. It is intended only for the individual(s) to whom it is addressed, and may not be saved, copied, printed, disclosed or used by anyone other than the intended recipient(s). If you are not an intended recipient, please delete this e-mail immediately and notify the sender by e-mail.

3 3

Uploading gzipped fastq files through the API
by dsobral＠igc.gulbenkian.pt 03 Jan '14

03 Jan '14

Hello, I have been using the galaxy API to upload files into a library (using a local folder for library import) and running a workflow into a history. I have been following the example scripts that come with galaxy. When I upload a gzipped fastq file, in autodetection mode (linking the file and not copying, to be faster), the file is not detected as fastq. Even if I explicitly say that it is a fastq, the file is uploaded as a fastq but with its contents gzipped (so downstream analysis fail). Nonetheless, if I do this manually through the interface, the file is unzipped correctly. Any idea how can I upload the gzipped fastq through the API so that it can be used properly? Thank you. ===================================== Daniel Sobral Next Generation Sequencing Data Analyst IGC - Instituto Gulbenkian de Ciencias e-mail dsobral(a)igc.gulbenkian.pt =====================================

3 2

ODoSE - error when using exclusively 'external' genomes
by Jen 03 Jan '14

03 Jan '14

hello, I've run across a possible bug in ODoSE that is preventing me from analyzing my data. I've scoured the various help documentation without luck, so I'm writing you. I'm using the program via this site: http://www.odose.nl/ The history showing the steps below is here: http://www.odose.nl/u/publ/h/unnamed-history The problem is this: I'm unable to work with a set of genomes that is exclusively "user-generated" (i.e., external, and uploaded from my local drive). To illustrate this problem with an example, I downloaded the .ffn files for four published genomes NCBI's ftp site. (This way, I'm sure my 'external' files are formatted correctly.) I've tried to follow these instructions from http://www.odose.nl/ (Analyze Data tab) - >"User-generated whole-genome data not yet archived in GenBank can be uploaded to be analysed separately or in conjunction with published genomes. To do this, first create a new history: in the right ‘History’ pane go to Options > Create New. In the left ‘Tools’ pane go to Get Data > Upload File and select one or multiple .ffn files from your computer and click ‘Execute’..." This worked fine. >"Go to Divergence > Upload genomes in the ‘Tools’ pane, press the ‘Add new genome’ button, specify a genome label and press ‘Execute’ for each genome to be included…" I was unable to find a "Divergence" option in the Tools pane. So, I assumed this should be O'DoSE > Upload Genomes, in the Tools Pane. Using this function, I uploaded each genome and selected "Execute." >"Proceed to the Workflow menu to add listed genomes and/or to specify input settings…" Perhaps this is my downfall, but I was unable to see how to add genomes in the Workflow menu. At this point, I had uploaded four genomes, and attempted to select the first option in the analysis: "Extract & Translate Genes." I chose the option of selecting my external genomes, but the analysis failed, giving the error "History does not include a dataset of the required format/build" error. This error appears within the "Genbank Project ID's" box. In this case, I have no Genbank Project ID's, because all data are external genomes. Interestingly: The problem is solved by selecting at least one genome from the Complete Microbial Genomes table. Selecting one genome generates a Project ID list. I am then able to perform "Extract & Translate Genes" and all further functions, acting on the set of external genomes and the one selected (internal) genome. I've tried this several times, with different external genome files. I can successfully analyze dozens of external genomes, but _only if_ at least one 'internal' genome is selected as well. I need to run an analysis on a set of genomes that is exclusively unpublished, so the data will be entirely "external" genomes. Including a published genome will throw off the comparisons we need to make. Based on the ODoSE instructions above (that user-generated whole-genome data...can be uploaded to be analysed separately or in conjunction with published genomes), I sense I should be able to use exclusively 'external' genomes in an analysis. Do you have any suggestions on how I can do this? Any advice would be much appreciated. thank you, Jen (Apologies to the moderator for the earlier version of this message that was too large. Above, I've removed the attachments showing screen shots. I hope the problem is clear from the History link above.)

2 1

Can REMOTE_USER be changed to another header variable?
by Prakash Velayutham 02 Jan '14

02 Jan '14

Hi, We have a SSO environment provided by Oracle Fusion products and for some reason, they don't like to send over HTTP_REMOTE_USER as a header variable to downstream servers. I have seen it before with other web sites I have integrated with Oracle Access Manager. Is there a way Galaxy can accept another HEADER variable than REMOTE_USER for its external authentication? As an extension: With just enabling HTTP_REMOTE_USER as a header variable from an external authenticator, Galaxy works without any issues. I tried this with a default Apache/mod_ldap/mod_authnz_ldap setup. However, when I mix the Oracle gateways into the mix, things break down. I made OAM send HTTP_AUTH_USER over to Galaxy. I changed all instances of REMOTE_USER to AUTH_USER in the installed location of Galaxy in my server. Authentication works fine, but I get issues with HISTORY part of Galaxy (below), when I access a workflow or basically any part of Galaxy that depends on HISTORY Error Traceback: View as: Interactive | Text | XML (full) AttributeError: 'NoneType' object has no attribute 'user' URL: http://xxx.xxx.xxx/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-d… Module weberror.evalexception.middleware:364 in respond view >> app_iter = self.application(environ, detect_start_response) Module paste.recursive:84 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.middleware.remoteuser:91 in __call__ view >> return self.app( environ, start_response ) Module paste.httpexceptions:633 in __call__ view >> return self.application(environ, start_response) Module galaxy.web.framework.base:132 in __call__ view >> return self.handle_request( environ, start_response ) Module galaxy.web.framework.base:190 in handle_request view >> body = method( trans, **kwargs ) Module galaxy.web.framework:98 in decorator view >> return func( self, trans, *args, **kwargs ) Module galaxy.webapps.galaxy.controllers.dataset:555 in list view >> status, message = self._copy_datasets( trans, hda_ids, target_histories ) Module galaxy.webapps.galaxy.controllers.dataset:1127 in _copy_datasets view >> if user != history.user: AttributeError: 'NoneType' object has no attribute 'user' Thanks, Prakash.

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Question about custom styling
by Daniel Patrick Sullivan 02 Jan '14

02 Jan '14

Hi, Galaxy Developers, I have searched the wiki and the mailing list and I can't seem to find an answer to this question (if there is a wiki page or a post that I missed, I apologize). Presumably there is a preferred way to do what I'm trying to do. I basically want to make some small cosmetic changes to Galaxy's CSS styling (base.css). These are very minor, and all involve overriding existing styles. I've successfully done this by copying the 'blue' theme, making my changes, and re-routing this though apache's redirect, for example: RewriteRule ^/static/style/(.*) /group/galaxy_test/galaxy-dist/static/MyCustom/$1 This is all find and good. It works. The problem is when I update galaxy. Things get kind of stagnant and changes from the repository are not propaged into my custom style. I noticed that there appear to be some theme generation script capabilities in galaxy-dist/static/style, for example make_style.py. There also appears to be some color stub ini file (blue_colors.ini). Whenever I try to launch make_style.py, it bombs out with: "NOTE: This script is no longer used for generating stylesheets" Invoking 'make INI=blue_colors.ini OUT=blue' instead. The execution of the referred to command fails with a parse errors on base.less and reset.less. So, I guess my question is: Is there a preferred method to override existing styling in base.css (of the blue template) such that modifications to the default style are merged in from Mercurial? I appreciate you taking the time to answer my question. Thank you so much I wish you a wonderful day. Dan Sullivan

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Re: [galaxy-dev] Can REMOTE_USER be changed to another header variable?
by Jennifer Jackson 02 Jan '14

02 Jan '14

Hi Prakash, You are on the thread so you should get direct replies. And you can review any of our mailing list postings by following the links here under "Archives": https://wiki.galaxyproject.org/MailingLists#The_lists Subscribing is optional, for posting or viewing. Thanks! Jen Galaxy team On 1/2/14 8:12 AM, Velayutham, Prakash (Prakash) wrote: > Hi, > > I guess I would have to subscribe to that list to get status updates? > > Thanks, > Prakash > > On Jan 2, 2014, at 11:09 AM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> > wrote: > >> Hello Prakash, >> I am going to move this over to the galaxy-dev(a)bx.psu.edu mailing >> list where it will have greater visibility within our development >> community. >> Best, >> Jen >> Galaxy team >> https://wiki.galaxyproject.org/MailingLists#The_lists >> >> On 1/2/14 7:27 AM, Velayutham, Prakash (Prakash) wrote: >>> Hi, >>> >>> We have a SSO environment provided by Oracle Fusion products and for >>> some reason, they don't like to send over HTTP_REMOTE_USER as a >>> header variable to downstream servers. I have seen it before with >>> other web sites I have integrated with Oracle Access Manager. Is >>> there a way Galaxy can accept another HEADER variable than >>> REMOTE_USER for its external authentication? >>> >>> As an extension: >>> >>> * With just enabling HTTP_REMOTE_USER as a header variable from an >>> external authenticator, Galaxy works without any issues. I tried >>> this with a default Apache/mod_ldap/mod_authnz_ldap setup. >>> * However, when I mix the Oracle gateways into the mix, things >>> break down. >>> o I made OAM send HTTP_AUTH_USER over to Galaxy. >>> o I changed all instances of REMOTE_USER to AUTH_USER in the >>> installed location of Galaxy in my server. >>> o Authentication works fine, but I get issues with HISTORY >>> part of Galaxy (below), when I access a workflow or >>> basically any part of Galaxy that depends on HISTORY >>> >>> >>> Error Traceback: >>> >>> View as: Interactive >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> | >>> Text >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> | >>> XML >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> (full) >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> ⇝ |AttributeError: 'NoneType' object has no attribute 'user'| >>> URL: >>> http://xxx.xxx.xxx/dataset/list?sort=-update_time&f-name=All&f-tags=All&f-d… >>> Module weberror.evalexception.middleware:*364* in |respond| <Mail >>> Attachment.jpeg> >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> view >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> |>> >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…>app_iter >>> *=* self*.*application*(*environ*,* detect_start_response*)*| >>> Module paste.recursive:*84* in |__call__| <Mail Attachment.jpeg> >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> view >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> |>> >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…>*return* >>> self*.*application*(*environ*,* start_response*)*| >>> Module galaxy.web.framework.middleware.remoteuser:*91* in |__call__| >>> <Mail Attachment.jpeg> >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> view >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> |>> >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…>*return* >>> self*.*app*(* environ*,* start_response *)*| >>> Module paste.httpexceptions:*633* in |__call__| <Mail >>> Attachment.jpeg> >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> view >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> |>> >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…>*return* >>> self*.*application*(*environ*,* start_response*)*| >>> Module galaxy.web.framework.base:*132* in |__call__| <Mail >>> Attachment.jpeg> >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> view >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> |>> >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…>*return* >>> self*.*handle_request*(* environ*,* start_response *)*| >>> Module galaxy.web.framework.base:*190* in |handle_request| <Mail >>> Attachment.jpeg> >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> view >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> |>> >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…>body >>> *=* method*(* trans*,* ****kwargs *)*| >>> Module galaxy.web.framework:*98* in |decorator| <Mail >>> Attachment.jpeg> >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> view >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> |>> >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…>*return* >>> func*(* self*,* trans*,* ***args*,* ****kwargs *)*| >>> Module galaxy.webapps.galaxy.controllers.dataset:*555* in |list| >>> <Mail Attachment.jpeg> >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> view >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> |>> >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…>status*,* >>> message *=* self*.*_copy_datasets*(* trans*,* hda_ids*,* >>> target_histories *)*| >>> Module galaxy.webapps.galaxy.controllers.dataset:*1127* in >>> |_copy_datasets| <Mail Attachment.jpeg> >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> view >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…> >>> |>> >>> <https://galaxy.research.cchmc.org/dataset/list?sort=-update_time&f-name=All…>*if* >>> user *!=* history*.*user*:*| >>> *AttributeError: 'NoneType' object has no attribute 'user'* >>> >>> Thanks, >>> Prakash >>> >>> >>> ___________________________________________________________ >>> The Galaxy User list should be used for the discussion of >>> Galaxy analysis and other features on the public server >>> atusegalaxy.org <http://usegalaxy.org>. Please keep all replies on the list by >>> using "reply all" in your mail client. For discussion of >>> local Galaxy instances and the Galaxy source code, please >>> use the Galaxy Development list: >>> >>> http://lists.bx.psu.edu/listinfo/galaxy-dev >>> >>> To manage your subscriptions to this and other Galaxy lists, >>> please use the interface at: >>> >>> http://lists.bx.psu.edu/ >>> >>> To search Galaxy mailing lists use the unified search at: >>> >>> http://galaxyproject.org/search/mailinglists/ >> >> -- >> Jennifer Hillman-Jackson >> http://galaxyproject.org > -- Jennifer Hillman-Jackson http://galaxyproject.org

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Local installation problem
by Cesar Rodriguez 02 Jan '14

02 Jan '14

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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