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Re: [galaxy-user] galaxy-user Digest, Vol 86, Issue 17
by Jun Fan 22 Aug '13

22 Aug '13

Hi Jen, Maybe I have not explained my question cleared which caused the confusion: I did not mean the name of dataset. Actually I asked about the display of the tool in the graphic view from the default value (guess it is the name attribute in the tool element of the wrapper) to something else in the workflow editor. As my ultimate purpose is to share my workflow with someone else. If they see three steps with the same displayed name and do not have the related knowledge, they will get lost. To help myself to explain well, here is the illustration: >From ------------------------------- ------------------------------- ------------------------------- | mzidLib:PostProcessing| | mzidLib:PostProcessing| | mzidLib:PostProcessing| |-----------------------------| |-----------------------------| |-----------------------------| | input file | ---------->| input file | ---------->| input file | |-----------------------------| | |-----------------------------| | |-----------------------------| |output (mzid) |----- |output (mzid) |----- |output (mzid) | ------------------------------- |-----------------------------| |-----------------------------| To ------------------------------------- ------------------------------------------- ------------------------------------------------ | mzidLib:PostProcessing FDR| | mzidLib:PostProcessing Threshold| | mzidLib:PostProcessing ProteoGroup| |----------------------------------| |------------------------------------------| |----------------------------------------------| | input file | ---------->| input file | ------------>| input file | |----------------------------------| | |------------------------------------------| | |----------------------------------------------| |output (mzid) |----- |output (mzid) |----- |output (mzid) | ----------------------------------- |------------------------------------------| |----------------------------------------------| Best regards! Jun Date: Tue, 20 Aug 2013 11:34:47 -0700 From: Jennifer Jackson <jen(a)bx.psu.edu> To: Jun Fan <j.fan(a)qmul.ac.uk> Cc: galaxy-user(a)lists.bx.psu.edu Subject: Re: [galaxy-user] customize tool display in the workflow Message-ID: <5213B6C7.5030800(a)bx.psu.edu> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" Hi Jun, You are very close - just click on the "create" button within the "Edit Step Actions" box and it will expand, where you can then enter the new custom name. It will look something like this: The other post you are referring to is a method to name the output dataset based on the input datasets name. You can certainly try this out and see if it is useful. Hope this helps, Jen Galaxy team On 8/20/13 9:34 AM, Jun Fan wrote: > Hi Jennifer, > > Many thanks for your reply. Unfortunately I am not clever to > figure out how to using the existing workflow dataset renaming > functions. I only know how to rename a dataset within history. Could > you show me how to do this? I have attached a screen shot of my > workflow. You can see that I have only managed to add annotation/notes > to this step. Ideally I would like to have the step with the label of > "mzidLib:PostProcessing FDR" in the graphic view. From other thread, > someone mentioned to use ${method} in the label, I failed to apply this trick. > > Best regards! > Jun > > Message: 3 > Date: Mon, 19 Aug 2013 10:18:32 -0700 > From: Jennifer Jackson <jen(a)bx.psu.edu> > To: Jun Fan <j.fan(a)qmul.ac.uk> > Cc: galaxy-user(a)lists.bx.psu.edu > Subject: Re: [galaxy-user] customize tool display in the workflow > Message-ID: <52125368.1060308(a)bx.psu.edu> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > Hi Jun, > > I asked Dannon (our workflow lead developer) and he suggested just > using the existing workflow datastet renaming functions. These are in > the right panel when you click on a dataset within the workflow editor > (as you probably know). > > Inherited naming is not something that is currently being worked on, > but you can always start a Trello card and see if it gathers votes or > the attention of a contributor from the larger development community: > http://wiki.galaxyproject.org/Support#Galaxy_Issue_Board > > Take care, > > Jen > Galaxy team > > On 8/18/13 5:11 PM, Jun Fan wrote: >> Dear Galaxy develop team: >> >> Normally I generate the workflow from history. It works fine >> except one annoying problem: the display of step/tool is just the >> tool name, which can cause confusion in a big workflow. For example, >> I have a mixture of samples from multiple species and do the BLAST >> against Human, Virus, Mouse etc which will call BLAST several times. >> To make results distinguishable, I will rename the dataset in the >> history. But this will be lost when creating workflow from history. >> The workflow will have duplicate steps named as BLAST while I really >> want to have steps displayed as BLAST against Human etc. Could you >> tell me whether I have done something wrong? If not, could you kindly >> add this functionality into the new release of Galaxy? If it is >> possible to customize the tool display in the workflow, how to write >> the wrapper as setting the label to allow this? >> >> Best regards! >> >> Jun >> >> >> >> ___________________________________________________________ >> 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 > > -------------- next part -------------- An HTML attachment was > scrubbed... > URL: > <http://lists.bx.psu.edu/pipermail/galaxy-user/attachments/20130819/8d > ca342d > /attachment-0001.html> > > ------------------------------ > > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > > End of galaxy-user Digest, Vol 86, Issue 16 > ******************************************* > > > ___________________________________________________________ > 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

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Re: [galaxy-user] customize tool display in the workflow
by Jun Fan 22 Aug '13

22 Aug '13

Hi Jen, First of all, please accept my sincere apology that I forgot to change the email title and made a mess Maybe I have not explained my question cleared which caused the confusion: I did not mean the name of dataset. Actually I asked about the display of the tool in the graphic view from the default value (guess it is the name attribute in the tool element of the wrapper) to something else in the workflow editor. As my ultimate purpose is to share my workflow with someone else. If they see three steps with the same displayed name and do not have the related knowledge, they will get lost. To help myself to explain well, please see the attached illustration. Best regards! Jun -----Original Message----- From: galaxy-user-bounces(a)lists.bx.psu.edu [mailto:galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of galaxy-user-request(a)lists.bx.psu.edu Sent: Wednesday, August 21, 2013 5:00 PM To: galaxy-user(a)lists.bx.psu.edu Subject: galaxy-user Digest, Vol 86, Issue 17 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..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-user Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. Question about Extract intron sequences from [gtf file] + [genome FASTA file] (??) 2. Re: Question about Extract intron sequences from [gtf file] + [genome FASTA file] (Jennifer Jackson) 3. Re: customize tool display in the workflow (Jun Fan) 4. Re: customize tool display in the workflow (Jennifer Jackson) 5. Very very slow response when a class is using Galaxy from a computer room in the university (Ido Carmel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 21 Aug 2013 00:29:56 +0800 From: ?? <zhusy88(a)msn.cn> To: <galaxy-user(a)lists.bx.psu.edu> Subject: [galaxy-user] Question about Extract intron sequences from [gtf file] + [genome FASTA file] Message-ID: <BLU176-DS19B84F8B1D1040DB7AA3E5C4430(a)phx.gbl> Content-Type: text/plain; charset="gb2312" Dear Jen, I am not much of a Galaxy user yet. Some days ago I know something about Galaxy and found it a really wonderful tool. And I am confused by a simple question regarding how to extract intron sequences from [gtf file]; Here is a simple of a gtf file: 1 Cufflinks transcript 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; 1 Cufflinks exon 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; exon_number "1"; 1 Cufflinks transcript 10 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; 1 Cufflinks exon 10 15 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1"; 1 Cufflinks exon 30 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1"; I want to extract intron from the [gtf] file. I found 2 ways may solve the question but it is both useless; 1. I use (Filter and Sort) -> Filter to cut the [gtf] file into 2 files such as the follows: File A ( contain transcript ): 1 Cufflinks transcript 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; 1 Cufflinks transcript 10 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; File B ( contain exon): 1 Cufflinks exon 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; exon_number "1"; 1 Cufflinks exon 10 15 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1"; 1 Cufflinks exon 30 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1"; Then I use (Operate on Genomic Intervals)->Subtract to subtract File B from File A Return Non-overlapping pieces of intervals. I thought it will return a file containing intron But the result is an empty file; 2. I convert [gtf] file to [Bed] file ,and use (Extract Features)->Gene BED To Exon/Intron/Codon BED, and it return the same result, an empty file. I think it must be something wrong with my thoughts. So I really need your help. Thank you very much. sincerely yours, John

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Re: [galaxy-user] Question about Extract intron sequences from [gtf file] + [genome FASTA file]
by 师云 22 Aug '13

22 Aug '13

Hi Jen, Thank you very much for your reply. The file contains more than 5000 transcripts so I don't pull out data per transcript. I do as you told and make sure the format. I filter the gff file to get a new file only containing exons information (I was wrong yesterday because I used the raw gtf file as I told in the former mail), then convert gtf to bed . So I can use (Extract Features)->Gene BED To Exon/Intron/Codon BED to get a bed file containing introns such like this: 1 9162341 9162884 CUFF.1911.1 0 - 1 22819814 22826251 CUFF.5109.1 0 + 1 25887852 25895755 CUFF.5509.1 0 - 1 25895822 25902258 CUFF.5509.1 0 - 1 39783161 39786032 CUFF.8086.1 0 + Then I met another problem: I got an empty file when I used Extract Genomic DNA to fetch sequence whether the file was gtf format or not. It returned a right result while I used the bed file downloaded from UCSC main. I think I have checked the format, but I found nothing wrong. the data downloaded from UCSC main is like this: chr1 133903980 133904133 NM_214429_exon_0_0_chr1_133903981_f 0 + chr1 133914112 133914267 NM_214429_exon_1_0_chr1_133914113_f 0 + chr1 133917280 133917449 NM_214429_exon_2_0_chr1_133917281_f 0 + Then I suddenly found the problem when I was trying to explain it. The input file of the tool (Extract Genomic DNA) request the condition of the chromosome name which should be ,for example, 'chr1' rather than '1' . I have tackled it all day .It is really low deficient when there is not anybody instructing in face to face. Best, John From: 师云 Sent: Wednesday, August 21, 2013 6:50 PM To: Jennifer Jackson Subject: Re: [galaxy-user] Question about Extract intron sequences from [gtf file] + [genome FASTA file] Hi Jen, Thank you very much for your reply. The file contains more than 5000 transcripts so I don't pull out data per transcript . I do as you say and make sure the format. I filter the gff file to get a new file only containing exons information (I was wrong yesterday because I used the raw gtf file as I told in the former mail), then convert gtf to bed . So I can use (Extract Features)->Gene BED To Exon/Intron/Codon BED to get a bed file containing introns such like this: 1 9162341 9162884 CUFF.1911.1 0 - 1 22819814 22826251 CUFF.5109.1 0 + 1 25887852 25895755 CUFF.5509.1 0 - 1 25895822 25902258 CUFF.5509.1 0 - 1 39783161 39786032 CUFF.8086.1 0 + Then I met another problem: I got an empty file when I used Extract Genomic DNA to fetch sequence whether the file was gtf format or not. It returned a right result while I used the bed file downloaded from UCSC main. I think I have checked the format, but I found nothing wrong. the data downloaded from UCSC main is like this: chr1 133903980 133904133 NM_214429_exon_0_0_chr1_133903981_f 0 + chr1 133914112 133914267 NM_214429_exon_1_0_chr1_133914113_f 0 + chr1 133917280 133917449 NM_214429_exon_2_0_chr1_133917281_f 0 + I have tackled it all day .It is really of low deficiency when there is not anybody instructing in face to face. So I need some of your tips. Best, John From: Jennifer Jackson Sent: Wednesday, August 21, 2013 1:45 AM To: 师云 Cc: galaxy-user(a)lists.bx.psu.edu Subject: Re: [galaxy-user] Question about Extract intron sequences from [gtf file] + [genome FASTA file] Hello, There appears to be something odd with the formatting of the GTF file - the exon counts are off in the second transcript's first exon. The exon_number "1" should be "2" (remember to count reverse, is on the negative strand). But that is a side issue. There are other things that do not quite make sense, but the entire dataset was not shared. Run this again, but do the following: 1 - make sure the files are in interval format and that the column assignments are correct (click on the pencil icon) 2 - Use strand assignment or better, separate (+) and (-) stranded transcripts into two files, at the start and run the query in two workflows from there. Some GOPS tools work best this way. Also, be aware that some of these transcripts will not have intron output. For example, the first transcript in your example is a single exon transcript. Also, if you have genes with overlapping variant transcripts, these will interfere with the query (you will lose introns or fractions of introns), but I don't know how large of a dataset you are working with. If you want to pull out data per transcript, the tools in the group "Filter and Sort" can be used to subset GFF/GTF files. The last query that you ran is the ideal way to run to obtain this information in Galaxy, but the GFF to BED converter creates a BED6, not a BED12 file, and this is why the tool produced no output (see the tool form for required input). Having this tool accept GTF formatted input might be something to consider as an enhancement - I will run it by our development team and open a Trello ticket as appropriate. Another method, which may not be available to you, (from looking at the chromosome identifiers - these are not UCSC chrom IDs) -- but could help in the future or others now, is to use the UCSC Table browser. It goes something like this: 1 - Click on "display at UCSC Main" for a GTF dataset, this loads the data as a custom track, default display in assembly viewer 2 - Once in UCSC, at the top bar, pick Tools -> Table Browser 3 - In the Table Browser, change track group to "Custom Tracks" and the user track you just loaded will be there 4 - Change region = genome, then output = bed, and make sure "Send output to Galaxy" is checked, submit 5 - On the next form, you will be given a list of regions to output in the BED6 output, Introns are one of them Best, Jen Galaxy team On 8/20/13 9:29 AM, 师云 wrote: Dear Jen, I am not much of a Galaxy user yet. Some days ago I know something about Galaxy and found it a really wonderful tool. And I am confused by a simple question regarding how to extract intron sequences from [gtf file]; Here is a simple of a gtf file: 1 Cufflinks transcript 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; 1 Cufflinks exon 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; exon_number "1"; 1 Cufflinks transcript 10 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; 1 Cufflinks exon 10 15 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1"; 1 Cufflinks exon 30 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1"; I want to extract intron from the [gtf] file. I found 2 ways may solve the question but it is both useless; 1. I use (Filter and Sort) -> Filter to cut the [gtf] file into 2 files such as the follows: File A ( contain transcript ): 1 Cufflinks transcript 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; 1 Cufflinks transcript 10 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; File B ( contain exon): 1 Cufflinks exon 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; exon_number "1"; 1 Cufflinks exon 10 15 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1"; 1 Cufflinks exon 30 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1"; Then I use (Operate on Genomic Intervals)->Subtract to subtract File B from File A Return Non-overlapping pieces of intervals. I thought it will return a file containing intron But the result is an empty file; 2. I convert [gtf] file to [Bed] file ,and use (Extract Features)->Gene BED To Exon/Intron/Codon BED, and it return the same result, an empty file. I think it must be something wrong with my thoughts. So I really need your help. Thank you very much. sincerely yours, John ___________________________________________________________ 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

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genome not available on galaxy
by Law, Michael J. 21 Aug '13

21 Aug '13

Hello, I am a new galaxy user and cannot find my reference genome in the drop down menu. I performed my ChIP seq experiments using S. cerevisiae SK1 strain background. Do you have that genome available for my analyses? Please let me know when you get a chance. Thanks, Mike Michael Law lawmj(a)rowan.edu<mailto:lawmj@rowan.edu>

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Re: [galaxy-user] customize tool display in the workflow
by Jun Fan 20 Aug '13

20 Aug '13

Hi Jennifer, Many thanks for your reply. Unfortunately I am not clever to figure out how to using the existing workflow dataset renaming functions. I only know how to rename a dataset within history. Could you show me how to do this? I have attached a screen shot of my workflow. You can see that I have only managed to add annotation/notes to this step. Ideally I would like to have the step with the label of "mzidLib:PostProcessing FDR" in the graphic view. From other thread, someone mentioned to use ${method} in the label, I failed to apply this trick. Best regards! Jun Message: 3 Date: Mon, 19 Aug 2013 10:18:32 -0700 From: Jennifer Jackson <jen(a)bx.psu.edu> To: Jun Fan <j.fan(a)qmul.ac.uk> Cc: galaxy-user(a)lists.bx.psu.edu Subject: Re: [galaxy-user] customize tool display in the workflow Message-ID: <52125368.1060308(a)bx.psu.edu> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" Hi Jun, I asked Dannon (our workflow lead developer) and he suggested just using the existing workflow datastet renaming functions. These are in the right panel when you click on a dataset within the workflow editor (as you probably know). Inherited naming is not something that is currently being worked on, but you can always start a Trello card and see if it gathers votes or the attention of a contributor from the larger development community: http://wiki.galaxyproject.org/Support#Galaxy_Issue_Board Take care, Jen Galaxy team On 8/18/13 5:11 PM, Jun Fan wrote: > > Dear Galaxy develop team: > > Normally I generate the workflow from history. It works fine > except one annoying problem: the display of step/tool is just the tool > name, which can cause confusion in a big workflow. For example, I have > a mixture of samples from multiple species and do the BLAST against > Human, Virus, Mouse etc which will call BLAST several times. To make > results distinguishable, I will rename the dataset in the history. But > this will be lost when creating workflow from history. The workflow > will have duplicate steps named as BLAST while I really want to have > steps displayed as BLAST against Human etc. Could you tell me whether > I have done something wrong? If not, could you kindly add this > functionality into the new release of Galaxy? If it is possible to > customize the tool display in the workflow, how to write the wrapper > as setting the label to allow this? > > Best regards! > > Jun > > > > ___________________________________________________________ > 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

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Question about Extract intron sequences from [gtf file] + [genome FASTA file]
by 师云 20 Aug '13

20 Aug '13

Dear Jen, I am not much of a Galaxy user yet. Some days ago I know something about Galaxy and found it a really wonderful tool. And I am confused by a simple question regarding how to extract intron sequences from [gtf file]; Here is a simple of a gtf file: 1 Cufflinks transcript 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; 1 Cufflinks exon 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; exon_number "1"; 1 Cufflinks transcript 10 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; 1 Cufflinks exon 10 15 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1"; 1 Cufflinks exon 30 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1"; I want to extract intron from the [gtf] file. I found 2 ways may solve the question but it is both useless; 1. I use (Filter and Sort) -> Filter to cut the [gtf] file into 2 files such as the follows: File A ( contain transcript ): 1 Cufflinks transcript 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; 1 Cufflinks transcript 10 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; File B ( contain exon): 1 Cufflinks exon 3 22 1000 + . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; exon_number "1"; 1 Cufflinks exon 10 15 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1"; 1 Cufflinks exon 30 40 1000 - . gene_id "CUFF.204"; transcript_id "CUFF.204.1"; exon_number "1"; Then I use (Operate on Genomic Intervals)->Subtract to subtract File B from File A Return Non-overlapping pieces of intervals. I thought it will return a file containing intron But the result is an empty file; 2. I convert [gtf] file to [Bed] file ,and use (Extract Features)->Gene BED To Exon/Intron/Codon BED, and it return the same result, an empty file. I think it must be something wrong with my thoughts. So I really need your help. Thank you very much. sincerely yours, John

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customize tool display in the workflow
by Jun Fan 19 Aug '13

19 Aug '13

Dear Galaxy develop team: Normally I generate the workflow from history. It works fine except one annoying problem: the display of step/tool is just the tool name, which can cause confusion in a big workflow. For example, I have a mixture of samples from multiple species and do the BLAST against Human, Virus, Mouse etc which will call BLAST several times. To make results distinguishable, I will rename the dataset in the history. But this will be lost when creating workflow from history. The workflow will have duplicate steps named as BLAST while I really want to have steps displayed as BLAST against Human etc. Could you tell me whether I have done something wrong? If not, could you kindly add this functionality into the new release of Galaxy? If it is possible to customize the tool display in the workflow, how to write the wrapper as setting the label to allow this? Best regards! Jun

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Questions about column output in Operate on genomic Intervals -> Profile Annotations
by James Wagner 19 Aug '13

19 Aug '13

Hello, I tried using this tool today after inputting a bed file containing 1509 intervals of 100 bp each, spread across all 22 autosomes. First of all, despite the fact that my input file contained intervals for 22 chromosomes, the value of "allCoverage" seemed to be the same as the value of the coverage of that table only for chr1. I was not really sure about the tableRegionCoverage column, as for most of the autosomes I had input data spread throughout the chromsome with points a few Mb away from either end, but I was getting a value in this column only about 1/3 of what I get when downloading the data directly from UCSC and summing the interval sizes. There were also many cases where nrCoverage > allCoverage, even when I reduced each input genomic interval to only 1 bp to avoid redundancy in the input file. Based on these descriptions of the columns I would expect allCoverage >= nrCoverage at all times. Just wondering if you could clarify what these columns are supposed to mean or how to reconcile these apparent inconsistencies.

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Uploading via FTP problem
by Delong, Zhou 19 Aug '13

19 Aug '13

Hello, I'm trying to upload some files via filezilla since Thursday and each time it fails after five or six hours of transfering and I cannot resume the transfer.. Every time I have the same errors: Status: Connection established, waiting for welcome message... Error: Connection timed out Error: Could not connect to server Each time it failes at different point so I don't think it's related to my files. Nor to the connection to the server, for I successfully downloaded some output data from the server (4 files, one of them was 20G). Is anyone experiencing the same problem or have an opinon on what's going on? Thanks, Delong

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Is anyone using Galaxy with NeuroScience ?
by Zeeshan Ali Shah 19 Aug '13

19 Aug '13

Hi, Is any one using galaxy for Neuroscience and brain imaging ? -- Regards Zeeshan Ali Shah System Administrator - PDC HPC PhD researcher (IT security) Kungliga Tekniska Hogskolan +46 8 790 9115 http://www.pdc.kth.se/members/zashah

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