April 2010 - galaxy-user - lists.galaxyproject.org

Internal Server Error
by Rathi Thiagarajan 08 Apr '10

08 Apr '10

Hi there, Just letting you know that there appears to be an internal server error. Time: 7:30pm EDT Thursday 8th of April Cheers Rathi

2 1

Re: [galaxy-user] galaxy-user Digest, Vol 46, Issue 5
by Peter Andrews 08 Apr '10

08 Apr '10

I also find that uploading a file rarely works -- it just displays the loading up blue arrow forever. On 4/7/2010 9:23 PM, galaxy-user-request(a)lists.bx.psu.edu wrote: > Send galaxy-user mailing list submissions to > galaxy-user(a)lists.bx.psu.edu > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.bx.psu.edu/listinfo/galaxy-user > or, via email, send a message with subject or body 'help' to > galaxy-user-request(a)lists.bx.psu.edu > > You can reach the person managing the list at > galaxy-user-owner(a)lists.bx.psu.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of galaxy-user digest..." > > > Today's Topics: > > 1. Re: Upload file (Daniel Blankenberg) > 2. Re: Upload file (Yanwei Tan) > 3. Re: Upload file (Daniel Blankenberg) > 4. Problem w/Cheetah, repeating dataset input (Jesse Erdmann) > 5. Re: Quality based trimming (Florent Angly) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 7 Apr 2010 09:53:19 -0400 > From: Daniel Blankenberg<dan(a)bx.psu.edu> > To: Yanwei Tan<Tan(a)nbio.uni-heidelberg.de> > Cc:galaxy-user@lists.bx.psu.edu > Subject: Re: [galaxy-user] Upload file > Message-ID:<37031484-8E2E-4A9C-A027-D0D75F8D0799(a)bx.psu.edu> > Content-Type: text/plain; charset=us-ascii > > Hi Wei, > > 3Gb is not that large of a file and should upload without issue. How are you uploading the file? - May I suggest that you try placing the file in a web-accessable location and provide the url to the upload tool in the paste box. > > Galaxy does accept the upload of individual gzipped files which can greatly reduce the time required for the transfer. > > Thanks, > > Dan > > > On Apr 6, 2010, at 6:04 PM, Yanwei Tan wrote: > > >> Hi Dan, >> >> Here I met a problem regarding the speed of upload file into Galaxy. Since my data is around 3G fastq file, I uploaded two days ago, the uploading still did not finish yet. I was wondering if I should try the zip compressed file. >> >> Many thanks! >> Wei >> >> On 4/6/10 5:00 PM, Daniel Blankenberg wrote: >> >>> Hi Florent, >>> >>> Thanks very much for the comments. A sliding window sounds like an excellent approach: allow users to specify the window size, step size, an aggregation action to perform on the window (min, max, sum, mean, etc ), a comparison method (<,<=, ==, etc) and a threshold quality value; allowing users to specify the ends (both or only one or the other) to trim would also likely be useful. Would it also be desirable to allow specifying a number of quality scores that can be excluded from the aggregation action (the zero low quality base pairs in your example)? A window size of 1 would handle the simple case of only trimming the very ends while allowing the user to configure more complex windowing schemes. Thoughts? >>> >>> Thanks, >>> >>> Dan >>> >>> On Apr 6, 2010, at 4:00 AM, Florent Angly wrote: >>> >>> >>> >>>> Thanks for your reply Daniel. >>>> >>>> >>>>> You are correct that there is not currently a tool to trim directly by quality in Galaxy; currently the the Summary statistics and boxplot tools are used to determine good cut off for use in the trim by column tool; percentage of read length can be more useful on variable length reads. However, adding a tool that can directly trim reads based upon a threshold quality score seems like a natural fit for Galaxy, when uniform read length is not present at the start and/or not a requirement at the end and the percentage-of-read-length method is not sufficient >>>>> >>>>> >>>>> >>>> That's right... I did not even think about using the boxplot tool to find how much to trim the ends. My reads all have the same length, but still, is seems more natural to only trim as much as needed and no more. For example, I have some reads that are completely low quality and should entirely trimmed/removed, whereas some might of good quality over almost all their length. >>>> >>>> >>>> >>>>> Lets verify that you are looking for something like this, where 'x' is a low quality base and 'o' is a high quality base: >>>>> Start with: >>>>> xxxooooxxooooxxx >>>>> after trimming ends for 'x': >>>>> ooooxxoooo >>>>> So that trimming happens only from the ends and stops as soon as a base above the threshold is found and internal low quality bases are not considered. >>>>> >>>>> >>>>> >>>> It's probaby better to use a short sliding window (of, say, 5 bp) and trim the ends until the window has no more than, say zero low quality base pairs. So, the following sequence would be converted from: >>>> xxxoxooooooxxooooooxoxxx >>>> to: >>>> ooooooxxoooooo >>>> >>>> Florent >>>> >>>> _______________________________________________ >>>> galaxy-user mailing list >>>> galaxy-user(a)lists.bx.psu.edu >>>> http://lists.bx.psu.edu/listinfo/galaxy-user >>>> >>>> >>> _______________________________________________ >>> galaxy-user mailing list >>> galaxy-user(a)lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-user >>> >>> >> -- >> Yanwei Tan >> Institute of Neurobiology >> 1.OG, AG Bading >> Im Neuenheimer Feld 364 >> University of Heidelberg >> 69120 Heidelberg >> Germany >> >> Tel:+49-6221-548319 >> Fax:+49-6221-546700 >> >> > > > ------------------------------ > > Message: 2 > Date: Wed, 07 Apr 2010 17:21:37 +0200 > From: Yanwei Tan<Tan(a)nbio.uni-heidelberg.de> > To: Daniel Blankenberg<dan(a)bx.psu.edu> > Cc:galaxy-user@lists.bx.psu.edu > Subject: Re: [galaxy-user] Upload file > Message-ID:<4BBCA301.80907(a)nbio.uni-heidelberg.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Dan, > > Many thanks for your reply. I just upload the file from my computer and > browse the location. If I upload the zip compressed file, should I > choose txtseq.zip format? My data is fastq file in txt file. And how > could I put the file in a web-accessible location? You mean the FTP server? > > Thanks for your help! > Wei > > > On 4/7/10 3:53 PM, Daniel Blankenberg wrote: > >> Hi Wei, >> >> 3Gb is not that large of a file and should upload without issue. How are you uploading the file? - May I suggest that you try placing the file in a web-accessable location and provide the url to the upload tool in the paste box. >> >> Galaxy does accept the upload of individual gzipped files which can greatly reduce the time required for the transfer. >> >> Thanks, >> >> Dan >> >> >> On Apr 6, 2010, at 6:04 PM, Yanwei Tan wrote: >> >> >> >>> Hi Dan, >>> >>> Here I met a problem regarding the speed of upload file into Galaxy. Since my data is around 3G fastq file, I uploaded two days ago, the uploading still did not finish yet. I was wondering if I should try the zip compressed file. >>> >>> Many thanks! >>> Wei >>> >>> On 4/6/10 5:00 PM, Daniel Blankenberg wrote: >>> >>> >>>> Hi Florent, >>>> >>>> Thanks very much for the comments. A sliding window sounds like an excellent approach: allow users to specify the window size, step size, an aggregation action to perform on the window (min, max, sum, mean, etc ), a comparison method (<,<=, ==, etc) and a threshold quality value; allowing users to specify the ends (both or only one or the other) to trim would also likely be useful. Would it also be desirable to allow specifying a number of quality scores that can be excluded from the aggregation action (the zero low quality base pairs in your example)? A window size of 1 would handle the simple case of only trimming the very ends while allowing the user to configure more complex windowing schemes. Thoughts? >>>> >>>> Thanks, >>>> >>>> Dan >>>> >>>> On Apr 6, 2010, at 4:00 AM, Florent Angly wrote: >>>> >>>> >>>> >>>> >>>>> Thanks for your reply Daniel. >>>>> >>>>> >>>>> >>>>>> You are correct that there is not currently a tool to trim directly by quality in Galaxy; currently the the Summary statistics and boxplot tools are used to determine good cut off for use in the trim by column tool; percentage of read length can be more useful on variable length reads. However, adding a tool that can directly trim reads based upon a threshold quality score seems like a natural fit for Galaxy, when uniform read length is not present at the start and/or not a requirement at the end and the percentage-of-read-length method is not sufficient >>>>>> >>>>>> >>>>>> >>>>>> >>>>> That's right... I did not even think about using the boxplot tool to find how much to trim the ends. My reads all have the same length, but still, is seems more natural to only trim as much as needed and no more. For example, I have some reads that are completely low quality and should entirely trimmed/removed, whereas some might of good quality over almost all their length. >>>>> >>>>> >>>>> >>>>> >>>>>> Lets verify that you are looking for something like this, where 'x' is a low quality base and 'o' is a high quality base: >>>>>> Start with: >>>>>> xxxooooxxooooxxx >>>>>> after trimming ends for 'x': >>>>>> ooooxxoooo >>>>>> So that trimming happens only from the ends and stops as soon as a base above the threshold is found and internal low quality bases are not considered. >>>>>> >>>>>> >>>>>> >>>>>> >>>>> It's probaby better to use a short sliding window (of, say, 5 bp) and trim the ends until the window has no more than, say zero low quality base pairs. So, the following sequence would be converted from: >>>>> xxxoxooooooxxooooooxoxxx >>>>> to: >>>>> ooooooxxoooooo >>>>> >>>>> Florent >>>>> >>>>> _______________________________________________ >>>>> galaxy-user mailing list >>>>> galaxy-user(a)lists.bx.psu.edu >>>>> http://lists.bx.psu.edu/listinfo/galaxy-user >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> galaxy-user mailing list >>>> galaxy-user(a)lists.bx.psu.edu >>>> http://lists.bx.psu.edu/listinfo/galaxy-user >>>> >>>> >>>> >>> >>> >> >> > > > ------------------------------ > > Message: 3 > Date: Wed, 7 Apr 2010 11:32:05 -0400 > From: Daniel Blankenberg<dan(a)bx.psu.edu> > To: Yanwei Tan<Tan(a)nbio.uni-heidelberg.de> > Cc:galaxy-user@lists.bx.psu.edu > Subject: Re: [galaxy-user] Upload file > Message-ID:<54E8CB9D-5C36-4A20-8C8A-188B3F908012(a)bx.psu.edu> > Content-Type: text/plain; charset=us-ascii > > Hi Wei, > > To upload a gzipped file (e.g. somefile.fastq.gz), just upload as you normally would (don't set to txtseq.zip - this is a special format), the file will be ungzipped automatically; zip files are not yet supported. > > As far as a web-accessible location, you can specify http(s) and ftp locations by entering e.g.http://someserver.org/somefile.fastq orftp://someserver.org/somefile.fastq into the 'paste' box in the upload tool, if you have access this type of resource. > > Thanks, > > Dan > > > On Apr 7, 2010, at 11:21 AM, Yanwei Tan wrote: > > >> Hi Dan, >> >> Many thanks for your reply. I just upload the file from my computer and browse the location. If I upload the zip compressed file, should I choose txtseq.zip format? My data is fastq file in txt file. And how could I put the file in a web-accessible location? You mean the FTP server? >> >> Thanks for your help! >> Wei >> >> >> On 4/7/10 3:53 PM, Daniel Blankenberg wrote: >> >>> Hi Wei, >>> >>> 3Gb is not that large of a file and should upload without issue. How are you uploading the file? - May I suggest that you try placing the file in a web-accessable location and provide the url to the upload tool in the paste box. >>> >>> Galaxy does accept the upload of individual gzipped files which can greatly reduce the time required for the transfer. >>> >>> Thanks, >>> >>> Dan >>> >>> >>> On Apr 6, 2010, at 6:04 PM, Yanwei Tan wrote: >>> >>> >>> >>>> Hi Dan, >>>> >>>> Here I met a problem regarding the speed of upload file into Galaxy. Since my data is around 3G fastq file, I uploaded two days ago, the uploading still did not finish yet. I was wondering if I should try the zip compressed file. >>>> >>>> Many thanks! >>>> Wei >>>> >>>> On 4/6/10 5:00 PM, Daniel Blankenberg wrote: >>>> >>>> >>>>> Hi Florent, >>>>> >>>>> Thanks very much for the comments. A sliding window sounds like an excellent approach: allow users to specify the window size, step size, an aggregation action to perform on the window (min, max, sum, mean, etc ), a comparison method (<,<=, ==, etc) and a threshold quality value; allowing users to specify the ends (both or only one or the other) to trim would also likely be useful. Would it also be desirable to allow specifying a number of quality scores that can be excluded from the aggregation action (the zero low quality base pairs in your example)? A window size of 1 would handle the simple case of only trimming the very ends while allowing the user to configure more complex windowing schemes. Thoughts? >>>>> >>>>> Thanks, >>>>> >>>>> Dan >>>>> >>>>> On Apr 6, 2010, at 4:00 AM, Florent Angly wrote: >>>>> >>>>> >>>>> >>>>> >>>>>> Thanks for your reply Daniel. >>>>>> >>>>>> >>>>>> >>>>>>> You are correct that there is not currently a tool to trim directly by quality in Galaxy; currently the the Summary statistics and boxplot tools are used to determine good cut off for use in the trim by column tool; percentage of read length can be more useful on variable length reads. However, adding a tool that can directly trim reads based upon a threshold quality score seems like a natural fit for Galaxy, when uniform read length is not present at the start and/or not a requirement at the end and the percentage-of-read-length method is not sufficient >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> That's right... I did not even think about using the boxplot tool to find how much to trim the ends. My reads all have the same length, but still, is seems more natural to only trim as much as needed and no more. For example, I have some reads that are completely low quality and should entirely trimmed/removed, whereas some might of good quality over almost all their length. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>>> Lets verify that you are looking for something like this, where 'x' is a low quality base and 'o' is a high quality base: >>>>>>> Start with: >>>>>>> xxxooooxxooooxxx >>>>>>> after trimming ends for 'x': >>>>>>> ooooxxoooo >>>>>>> So that trimming happens only from the ends and stops as soon as a base above the threshold is found and internal low quality bases are not considered. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> It's probaby better to use a short sliding window (of, say, 5 bp) and trim the ends until the window has no more than, say zero low quality base pairs. So, the following sequence would be converted from: >>>>>> xxxoxooooooxxooooooxoxxx >>>>>> to: >>>>>> ooooooxxoooooo >>>>>> >>>>>> Florent >>>>>> >>>>>> _______________________________________________ >>>>>> galaxy-user mailing list >>>>>> galaxy-user(a)lists.bx.psu.edu >>>>>> http://lists.bx.psu.edu/listinfo/galaxy-user >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> galaxy-user mailing list >>>>> galaxy-user(a)lists.bx.psu.edu >>>>> http://lists.bx.psu.edu/listinfo/galaxy-user >>>>> >>>>> >>>>> >>>> >>>> >>> >>> >> > > > ------------------------------ > > Message: 4 > Date: Wed, 7 Apr 2010 16:25:37 -0500 > From: Jesse Erdmann<jerdmann(a)umn.edu> > To:galaxy-user@bx.psu.edu > Subject: [galaxy-user] Problem w/Cheetah, repeating dataset input > Message-ID: > <m2h97174eb21004071425o9cba9384i648744371304d210(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi all, > > I'm using the following XML: > > ... > <inputs> > <param type="data" format="txt" name="seqmeta" label="PAPS.seqmeta"/> > <param type="data" format="txt" name="lib_info" label="Label Info"/> > <repeat name="to_merge" title="Evaluation Inputs and Results"> > <param type="select" name="pmm" label="Mismatch %" help="Maximum > % of mismatch between the construct sequence and the comparison > sequence."> > <option value="10">10%</option> > <option value="15">15%</option> > <option value="20">20%</option> > </param> > <param type="text" name="max_length" label="Max Construct Length" > value="25" /> > <param format="fasta" name="fasta_in" type="data" label="FastA Output"/> > <param format="txt" name="seq_stats" type="data" label="Sequence Stats"/> > </repeat> > </inputs> > ... > <configfiles> > <configfile name="file_info"> > #for $merge_set in enumerate( $to_merge ) > #silent sys.stderr.write($merge_set.__str__() + "\n") > #silent sys.stderr.write($merge_set.fasta_in.__str__()) > #end for > </configfile> > </configfiles> > ... > > And getting the resulting output: > > 127.0.0.1 - - [07/Apr/2010:15:31:50 -0500] "POST /admin/tool_reload > HTTP/1.1" 200 -"http://localhost:8080/admin/reload_tool" "Mozilla/5.0 > (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.2.2) Gecko/20100316 > Firefox/3.6.2" > 127.0.0.1 - - [07/Apr/2010:15:31:59 -0500] "POST /tool_runner/index > HTTP/1.1" 200 -"http://localhost:8080/tool_runner/index" "Mozilla/5.0 > (Macintosh; U; Intel Mac OS X 10.5; en-US; rv:1.9.2.2) Gecko/20100316 > Firefox/3.6.2" > galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-04-07 15:32:03,765 > RoundRobin queue: user/session did not exist, created new jobqueue for > session = 6 > galaxy.jobs DEBUG 2010-04-07 15:32:03,766 job 234 put in policy queue > galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-04-07 15:32:03,766 > RoundRobin queue: retrieving job from job queue for session = 6 > galaxy.jobs DEBUG 2010-04-07 15:32:03,766 dispatching job 234 to local runner > galaxy.jobs DEBUG 2010-04-07 15:32:05,423 job 234 dispatched > (0, {'seq_stats':<galaxy.tools.DatasetFilenameWrapper object at > 0x572b390>, '__index__': 0, 'max_length': > <galaxy.tools.InputValueWrapper object at 0x572b8d0>, 'fasta_in': > <galaxy.tools.DatasetFilenameWrapper object at 0x572b810>, 'pmm': > <galaxy.tools.SelectToolParameterWrapper object at 0x572b290>}) > 127.0.0.1 - - [07/Apr/2010:15:32:03 -0500] "GET /history HTTP/1.1" 200 > -"http://localhost:8080/tool_runner/index" "Mozilla/5.0 (Macintosh; > U; Intel Mac OS X 10.5; en-US; rv:1.9.2.2) Gecko/20100316 > Firefox/3.6.2" > galaxy.jobs.runners.local ERROR 2010-04-07 15:32:07,356 failure running job 234 > Traceback (most recent call last): > File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/jobs/runners/local.py", > line 55, in run_job > job_wrapper.prepare() > File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/jobs/__init__.py", > line 386, in prepare > config_filenames = self.tool.build_config_files( param_dict, > self.working_directory ) > File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/tools/__init__.py", > line 1364, in build_config_files > f.write( fill_template( template_text, context=param_dict ) ) > File "/Users/jerdmann/Python/galaxy-central/lib/galaxy/util/template.py", > line 9, in fill_template > return str( Template( source=template_text, searchList=[context] ) ) > File "/Users/jerdmann/Python/galaxy-central/eggs/Cheetah-2.2.2-py2.5-macosx-10.3-fat-ucs2.egg/Cheetah/Template.py", > line 1004, in __str__ > return getattr(self, mainMethName)() > File "cheetah_DynamicallyCompiledCheetahTemplate_1270672326_31_15888.py", > line 86, in respond > NotFound: cannot find 'fasta_in' while searching for 'merge_set.fasta_in' > > So, I'm printing the merge_set dictionary and seeing a fasta_in key, > but when I try to use fasta_in it can not be found. I'm assuming this > is probably a syntax oversight on my part, but I'm not seeing it. > > -- -------------- Peter Andrews Programmer Computational Genetics Lab Dartmouth Hitchcock Medical Center (603) 653-9963

3 2

Re: [galaxy-user] Upload file
by Daniel Blankenberg 07 Apr '10

07 Apr '10

Hi Wei, 3Gb is not that large of a file and should upload without issue. How are you uploading the file? - May I suggest that you try placing the file in a web-accessable location and provide the url to the upload tool in the paste box. Galaxy does accept the upload of individual gzipped files which can greatly reduce the time required for the transfer. Thanks, Dan On Apr 6, 2010, at 6:04 PM, Yanwei Tan wrote: > Hi Dan, > > Here I met a problem regarding the speed of upload file into Galaxy. Since my data is around 3G fastq file, I uploaded two days ago, the uploading still did not finish yet. I was wondering if I should try the zip compressed file. > > Many thanks! > Wei > > On 4/6/10 5:00 PM, Daniel Blankenberg wrote: >> Hi Florent, >> >> Thanks very much for the comments. A sliding window sounds like an excellent approach: allow users to specify the window size, step size, an aggregation action to perform on the window (min, max, sum, mean, etc ), a comparison method (<,<=, ==, etc) and a threshold quality value; allowing users to specify the ends (both or only one or the other) to trim would also likely be useful. Would it also be desirable to allow specifying a number of quality scores that can be excluded from the aggregation action (the zero low quality base pairs in your example)? A window size of 1 would handle the simple case of only trimming the very ends while allowing the user to configure more complex windowing schemes. Thoughts? >> >> Thanks, >> >> Dan >> >> On Apr 6, 2010, at 4:00 AM, Florent Angly wrote: >> >> >>> Thanks for your reply Daniel. >>> >>>> You are correct that there is not currently a tool to trim directly by quality in Galaxy; currently the the Summary statistics and boxplot tools are used to determine good cut off for use in the trim by column tool; percentage of read length can be more useful on variable length reads. However, adding a tool that can directly trim reads based upon a threshold quality score seems like a natural fit for Galaxy, when uniform read length is not present at the start and/or not a requirement at the end and the percentage-of-read-length method is not sufficient >>>> >>>> >>> That's right... I did not even think about using the boxplot tool to find how much to trim the ends. My reads all have the same length, but still, is seems more natural to only trim as much as needed and no more. For example, I have some reads that are completely low quality and should entirely trimmed/removed, whereas some might of good quality over almost all their length. >>> >>> >>>> Lets verify that you are looking for something like this, where 'x' is a low quality base and 'o' is a high quality base: >>>> Start with: >>>> xxxooooxxooooxxx >>>> after trimming ends for 'x': >>>> ooooxxoooo >>>> So that trimming happens only from the ends and stops as soon as a base above the threshold is found and internal low quality bases are not considered. >>>> >>>> >>> It's probaby better to use a short sliding window (of, say, 5 bp) and trim the ends until the window has no more than, say zero low quality base pairs. So, the following sequence would be converted from: >>> xxxoxooooooxxooooooxoxxx >>> to: >>> ooooooxxoooooo >>> >>> Florent >>> >>> _______________________________________________ >>> galaxy-user mailing list >>> galaxy-user(a)lists.bx.psu.edu >>> http://lists.bx.psu.edu/listinfo/galaxy-user >>> >> >> _______________________________________________ >> galaxy-user mailing list >> galaxy-user(a)lists.bx.psu.edu >> http://lists.bx.psu.edu/listinfo/galaxy-user >> > > > -- > Yanwei Tan > Institute of Neurobiology > 1.OG, AG Bading > Im Neuenheimer Feld 364 > University of Heidelberg > 69120 Heidelberg > Germany > > Tel:+49-6221-548319 > Fax:+49-6221-546700 >

2 2

unsubscribe
by Davide Corona 06 Apr '10

06 Apr '10

Could you please unsuscribe me? thank you best regards DAvide

5 4

unsuscribe
by Wood 06 Apr '10

06 Apr '10

Hi Could you please unsuscribe me? thank you best regards Olivier

2 1

"Edit Attributes" not working when logged in
by amit mandal 06 Apr '10

06 Apr '10

hello all, I've been using Galaxy for quite some time. Since last 2 weeks I'm unable to use the *Edit Attributes* (*pencil icon*) on the stored datasets when logged in my Galaxy account (this e-mail ID). If I use Galaxy without logging in, the *pencil icon* works fine. But as I log in and try to do the same, I get this message in the middle pane of the Galaxy site - " Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) " I've attached a screenshot for reference. Recently I updated my account from an old ID to this e-mail ID. Could the error be linked to this? There are several histories stored in my account. I'm unable to use the *pencil icon* in neither of them. Kindly help, I'm confused. thank you. regards, -- Amit Mandal Graduate Student Genomics & Molecular Medicine IGIB igib.in

1 0

converting file to interval or bed in a workflow
by Michael Wilson 05 Apr '10

05 Apr '10

Dear Galaxy users/developers, I was wondering if anyone knows a way to take a tabular file (i.e. with four columns: chr start stop name) and convert it into a bed or interval file during a workflow (as opposed to doing it manually). I have a workflow which produces a four-column tabular file by extracting columns from an input file but I need it to be recognized as a bed or interval in order to then extract sequences in fasta format. There may be something obvious I am missing but I do not see any options in the Convert formats tools. Thanks in advance. Cheers, Mike

1 0

Col 4?
by Desmond Lim 01 Apr '10

01 Apr '10

Hi, I'm using galaxy to download data from UCSC. The data has 4 columns, what is the 4 column? It states name but has chromosome numbers on it. Thanks. Desmond

2 1