Re: [galaxy-user] upload data to galaxy using terminal
I don't understand your question. What is stopping your from using the API from terminal? However the easiest way to do it would probably be with Python and the BioBlend project (http://bioblend.readthedocs.org/en/latest/ and https://github.com/afgane/bioblend). Another way is to set up a watcher in the folder that your tool is creating files in and upload to Galaxy on change. If none of these make sense to you please clarify your need. thanks Martin On Wed, Mar 26, 2014 at 2:27 AM, do kadya doka...@gmail.com wrote: Thank you very much Martin Čech for reply. Currently I am uploading data by using linking method only, But what I wanted is NO API, that means via terminal only. As you can see my first mail where I am explaining query, MuSiC2 creating folders and files by itself, and hence galaxy will not be able to track those files. hence I want to collect those files and upload to current history (as data sets) using Terminal. Is that thing is possible ? else how can I tell Galaxy that tool is creating folder first and then writing files ? I am usinghttp://cli-mate.lumc.nl/define#to create xml file for galaxy. I know I can hide output (from main command), but how can i track file which is inside folder ? Waiting for positive reply. On Tue, Mar 25, 2014 at 6:04 PM, Martin Čech mar...@bx.psu.edu wrote: Hi, yes, you can link files to a Galaxy Library without copying - please see https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles(the last part 'Upload files from filesystem paths'). And there is an API for libraries (although it is under construction). The flow of controllers for upload is api/library_contents controllers/library_common https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.library_contents Martin On Tue, Mar 25, 2014 at 7:47 AM, do kadya doka...@gmail.com wrote: Hi, Can I upload data (mostly link the data) using terminal ? MuSiC 2 tool integration is not available in their website nor in tool shed. MuSiC 2 creates folder and files by itself, which is hard to track by Galaxy. So is there any way to link files to galaxy current work space so that I can link those distracted files which are created by MuSiC 2. ex: if you run music2 bmr calc-bmrfile_of_input output is 3 files, ./file1.txt ./folder1/file2.txt ./folder2/file3.txt we can not mention that we need this output filename or save file at specific location, we can not give this option. Galaxy will not able to track this output, hence i have to do it manually. So is it possible to upload this files manually by terminal ? Waiting for positive reply. Thank You - Chetan ___ 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/ ___ 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/
Re: [galaxy-user] upload data to galaxy using terminal
Hi, yes, you can link files to a Galaxy Library without copying - please see https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles(the last part 'Upload files from filesystem paths'). And there is an API for libraries (although it is under construction). The flow of controllers for upload is api/library_contents controllers/library_common https://galaxy-central.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.library_contents Martin On Tue, Mar 25, 2014 at 7:47 AM, do kadya doka...@gmail.com wrote: Hi, Can I upload data (mostly link the data) using terminal ? MuSiC 2 tool integration is not available in their website nor in tool shed. MuSiC 2 creates folder and files by itself, which is hard to track by Galaxy. So is there any way to link files to galaxy current work space so that I can link those distracted files which are created by MuSiC 2. ex: if you run music2 bmr calc-bmrfile_of_input output is 3 files, ./file1.txt ./folder1/file2.txt ./folder2/file3.txt we can not mention that we need this output filename or save file at specific location, we can not give this option. Galaxy will not able to track this output, hence i have to do it manually. So is it possible to upload this files manually by terminal ? Waiting for positive reply. Thank You - Chetan ___ 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/ ___ 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/
Re: [galaxy-user] Data Uploading through FTP
Hello Scott, there is no 'new Galaxy' that has changed the way upload works. If you were able to upload files before the February release just follow the same path. The only thing that evolved is that we added another way to upload files that we are planning to replace the old one with - but that will happen in the future. So to reiterate once more: You can use the 'old upload' that is intact under Get Data / Upload File on the usegalaxy.org server if you have trouble using the new one. If you have trouble using the new one please post a specific question about it. Please do not reply to other threads with an unrelated question. Thank you Martin On Fri, Mar 14, 2014 at 11:24 AM, Scott Tighe scott.ti...@uvm.edu wrote: Hi Galaxy List If anybody has some insight as to how to upload data to the new Galaxy, I sure would enjoy hearing the trick. Scott Scott Tighe Senior Core Laboratory Research Staff Advanced Genome Technologies Core NextGen Sequencing/Flow Cytometry University of Vermont and Vermont Cancer Center 149 Beaumont ave Health Science Research Facility 303/305 Burlington Vermont 05405 802-656-2482 (AGTC) On 3/14/2014 10:25 AM, Jennifer Jackson wrote: Hi Elvio, Peter is correct - you can manage any list membership through the mailman web pages. I found you only on this list and unsubscribed you. If you want to instead consider the galaxy-announce mailing list (low volume, general project updates), links for how to sign up are on this wiki: https://wiki.galaxyproject.org/MailingLists Best, Jen Galaxy team On 3/14/14 2:58 AM, Elvio Pederzolli wrote: Hi there can you please unsubscribe me from all Galaxy lists please Thank you Elvio Pederzolli Sent from my iPad ___ 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/ ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-user] Data Uploading through FTP
Scott: 15GB file is a candidate for a FTP upload because web browsers can't usually handle this size. FTP server address is usegalaxy.org and credentials are the same you use for Galaxy (you have to use some other client outside of web browser to connect to this FTP server and upload this large file successfully e.gg FileZilla). After you finish uploading your file there you will see it in the upload tool (Get Data / Upload File) on Galaxy (when logged in). Then you will be able to start using it in history. There is an awesome screencast that shows the full process here: http://vimeo.com/75938324 Martin On Fri, Mar 14, 2014 at 1:48 PM, Scott Tighe scott.ti...@uvm.edu wrote: Martin One other thing. I believe you are incorrect about uploading using the usegalaxy.org page with a 15 gb file. That I believe that is a mistake by the Galaxy team. Maybe a clear tutorial on how to upload a 15gb file would be nice. Thanks Again Scott Scott Tighe Senior Core Laboratory Research Staff Advanced Genome Technologies Core NextGen Sequencing/Flow Cytometry University of Vermont and Vermont Cancer Center 149 Beaumont ave Health Science Research Facility 303/305 Burlington Vermont 05405 802-656-2482 (AGTC)On 3/14/2014 12:52 PM, Martin Čech wrote: Hello Scott, there is no 'new Galaxy' that has changed the way upload works. If you were able to upload files before the February release just follow the same path. The only thing that evolved is that we added another way to upload files that we are planning to replace the old one with - but that will happen in the future. So to reiterate once more: You can use the 'old upload' that is intact under Get Data / Upload File on the usegalaxy.org server if you have trouble using the new one. If you have trouble using the new one please post a specific question about it. Please do not reply to other threads with an unrelated question. Thank you Martin On Fri, Mar 14, 2014 at 11:24 AM, Scott Tighe scott.ti...@uvm.edu wrote: Hi Galaxy List If anybody has some insight as to how to upload data to the new Galaxy, I sure would enjoy hearing the trick. Scott Scott Tighe Senior Core Laboratory Research Staff Advanced Genome Technologies Core NextGen Sequencing/Flow Cytometry University of Vermont and Vermont Cancer Center 149 Beaumont ave Health Science Research Facility 303/305 Burlington Vermont 05405 802-656-2482 (AGTC) On 3/14/2014 10:25 AM, Jennifer Jackson wrote: Hi Elvio, Peter is correct - you can manage any list membership through the mailman web pages. I found you only on this list and unsubscribed you. If you want to instead consider the galaxy-announce mailing list (low volume, general project updates), links for how to sign up are on this wiki: https://wiki.galaxyproject.org/MailingLists Best, Jen Galaxy team On 3/14/14 2:58 AM, Elvio Pederzolli wrote: Hi there can you please unsubscribe me from all Galaxy lists please Thank you Elvio Pederzolli Sent from my iPad ___ 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/ ___ 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/ ___ 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
Re: [galaxy-user] large data to upload problem
Hello Chetan, Björn sent you a different link yesterday. Please read through it - especially this part: *Upload files from filesystem paths*. https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles M. On Tue, Feb 25, 2014 at 5:37 AM, do kadya doka...@gmail.com wrote: Hi, Thank You for reply. I am still not clear about this website. https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP There are total 4 main points highlighted in this website. Do I have to follow all 4 points ? I have tried just on second point which is Configuring Galaxy As I just need same folder for galaxy where I can put my content directly. Now after sometime I will all of the points mentioned. Next Question is WHY GALAXY IS NOT ACCEPTING .bai files? .bai is indexed form of .bam files. I tried uploading using admin section upload, which not worked. next normal file upload as .bai file is just 6 MB., but not worked. next I write xml file to incorporate samtools index into galaxy. Program run successfully but output file is 0 KB. in all of my try .bai file is 0 KB. I need to upload because my 'x' program is not accepting normal BAM format hence it needs Indexed BAM. Waiting for positive reply. On Tue, Feb 25, 2014 at 1:08 PM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi Do, the link I send you yesterday, contains a section about linking file. Have a close look at the upload form in the admin section. There should be an option to link the file into Galaxy. As a side note, I really think you will need an additional harddrive, 100GB free space would be not enough, imho. Cheers, Bjoern Hi, Thank You for answers, I am able to learn everyday. I am having 500 GB hard disk, I am trying to integrate 'x' tool to galaxy for local lab purpose. 'x' tool require bam files which are of 400 GB file size. When I used Admin section to upload file my computer hang because of no space. Is it way that I can tell Galaxy that use these files directly or may be I can convert files to Galaxy required format so that galaxy will not create files by itself. As you can see in my example, I am having 500 GB HDD, and ~400 GB BAM files, replication of data by Galaxy its not possible for me. Some option like tell Galaxy about extension and properties of file, so that it should not replicate. By command line 'x' is working fine. Need some really good solution. Waiting for positive reply. Thank You. -- Reagrds, Chetan doka...@gmail.com ___ 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/ -- Regards, Chetan ___ 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/ ___ 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/
Re: [galaxy-user] upload more than 2GB data from local computer to local installation of galaxy
Hello, Björn is exactly right. Link the data to Galaxy as described on the wiki page he posted. If you want to run FTP server with Galaxy (it is not included by default) you have to install and configure it yourself. Here is a wikipage that will show you how to do it. https://wiki.galaxyproject.org/Admin/Config/Upload%20via%20FTP However if you plan to work with such large files on local machine you might easily end up having to wait for a loong time, depending on what you plan to do with it and what are specifications of the machine. Consider cloud (https://wiki.galaxyproject.org/CloudMan) or public instance ( usegalaxy.org). Martin On Mon, Feb 24, 2014 at 5:30 AM, Björn Grüning bjoern.gruen...@gmail.comwrote: Hi Do, If you are running a loacl instance and you are admin you can use the data library and upload or even better link your data into a data library. https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles Cheers, Bjoern Hi, I am unable to upload more than 3 GB data from local computer to local installation of galaxy. How can I do that ? I saw many of the tutorials which says about online upload. My Galaxy is running on 127.0.0.7:8080 I tried FileZilla to upload file, but its says Connection established, waiting for welcome message and after some time ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-user] Galaxy job is waiting to run forever
Hello Martina, how did you try to upload it and on what server? I assume it was usegalaxy.org but please confirm. DId you use the upload button on the main page or *Get Data / Upload File* from the tool menu? How big is the file? thanks Martin, Galaxy team On Mon, Feb 17, 2014 at 11:37 AM, Martina Kracikova martina_kracik...@yahoo.co.uk wrote: Hello, I tried to upload some fasq data but the jobs never started running and I waited over 20 hours. I deleted them but now even very small jobs in the Galaxy 101 tutorial never start running. My colleague tried to execute the same job in the tutorial and it finished in less than a minute, so is this something to do with my account? I'm a registered user and am only using 8.4MB and am only trying to run 1 job. I would appreciate any help. Thank you! ___ 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/ ___ 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/
Re: [galaxy-user] Galaxy job is waiting to run forever
Hi Martina, this is the actual URL of the file: ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA046/SRA046351/SRX099052/SRR349685.fastq.bz2 The URL that you were using is the link to the folder, not the file (you can tell e.g. by the suffix of the file - my link has it, yours does not). Please try the new link and let me know if you encounter any problems. Goodluck. thank you for using Galaxy! Martin, Galaxy team On Mon, Feb 17, 2014 at 2:23 PM, Martina Kracikova martina_kracik...@yahoo.co.uk wrote: Hi Martin, Yes, I used usegalaxy.org. I uploaded the data from Get Data, Upload File and then pasted this link and selected FASTQ as file format: ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA046/SRA046351/SRX099052 It should be 337MB. The job was running for over 20 hours and never finished, so I eventually deleted it. Now I can't run any other jobs, not even a small job from the Galaxy 101 tutorial (Sort on data 4 has been waiting to run for over 2 hours now), which on my colleague's computer took less than a minute to finish. This makes me think it's something specific to my account. Thanks for your help! Martina On Monday, February 17, 2014 1:36 PM, Martin Čech mar...@bx.psu.edu wrote: Hello Martina, how did you try to upload it and on what server? I assume it was usegalaxy.org but please confirm. DId you use the upload button on the main page or *Get Data / Upload File* from the tool menu? How big is the file? thanks Martin, Galaxy team On Mon, Feb 17, 2014 at 11:37 AM, Martina Kracikova martina_kracik...@yahoo.co.uk wrote: Hello, I tried to upload some fasq data but the jobs never started running and I waited over 20 hours. I deleted them but now even very small jobs in the Galaxy 101 tutorial never start running. My colleague tried to execute the same job in the tutorial and it finished in less than a minute, so is this something to do with my account? I'm a registered user and am only using 8.4MB and am only trying to run 1 job. I would appreciate any help. Thank you! ___ 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/ ___ 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/
Re: [galaxy-user] Galaxy job is waiting to run forever
Martina: it seems that the server you are downloading from has troubles communicating with Galaxy. This is probably FTP issue that we cannot control. The workaround is to download it yourself to your computer from the site and then upload it to Galaxy directly. Let me know how it goes regards Martin, Galaxy team On Mon, Feb 17, 2014 at 3:12 PM, Martina Kracikova martina_kracik...@yahoo.co.uk wrote: Hi Martin, Unfortunately, this job also isn't running (I'm attaching a screen shot of the job queue). I also got a new error message saying that Galaxy couldn't be reached (I'm attaching that too), perhaps that's the problem? Thank you, Martina On Monday, February 17, 2014 2:32 PM, Martin Čech mar...@bx.psu.edu wrote: Hi Martina, this is the actual URL of the file: ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA046/SRA046351/SRX099052/SRR349685.fastq.bz2 The URL that you were using is the link to the folder, not the file (you can tell e.g. by the suffix of the file - my link has it, yours does not). Please try the new link and let me know if you encounter any problems. Goodluck. thank you for using Galaxy! Martin, Galaxy team On Mon, Feb 17, 2014 at 2:23 PM, Martina Kracikova martina_kracik...@yahoo.co.uk wrote: Hi Martin, Yes, I used usegalaxy.org. I uploaded the data from Get Data, Upload File and then pasted this link and selected FASTQ as file format: ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA046/SRA046351/SRX099052 It should be 337MB. The job was running for over 20 hours and never finished, so I eventually deleted it. Now I can't run any other jobs, not even a small job from the Galaxy 101 tutorial (Sort on data 4 has been waiting to run for over 2 hours now), which on my colleague's computer took less than a minute to finish. This makes me think it's something specific to my account. Thanks for your help! Martina On Monday, February 17, 2014 1:36 PM, Martin Čech mar...@bx.psu.edu wrote: Hello Martina, how did you try to upload it and on what server? I assume it was usegalaxy.org but please confirm. DId you use the upload button on the main page or *Get Data / Upload File* from the tool menu? How big is the file? thanks Martin, Galaxy team On Mon, Feb 17, 2014 at 11:37 AM, Martina Kracikova martina_kracik...@yahoo.co.uk wrote: Hello, I tried to upload some fasq data but the jobs never started running and I waited over 20 hours. I deleted them but now even very small jobs in the Galaxy 101 tutorial never start running. My colleague tried to execute the same job in the tutorial and it finished in less than a minute, so is this something to do with my account? I'm a registered user and am only using 8.4MB and am only trying to run 1 job. I would appreciate any help. Thank you! ___ 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/ ___ 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/
Re: [galaxy-user] Transcriptome Hypericum perforatum
Hello Miro, for these kind of general questions I would recommend you to ask in the bioinformatics forum at http://www.biostars.org/ as it is somewhat unrelated to Galaxy. Nevertheless some of the tools you mentioned are installed and available on the main instance (usegalaxy.org) and some you can install on your own Galaxy via the Toolshed (http://toolshed.g2.bx.psu.edu/). best Martin, Galaxy Team On Mon, Nov 25, 2013 at 4:16 PM, miroslav.sotak miroslav.so...@upjs.skwrote: To whom it may concern I would like to kindly ask you if you do have any experience in de-novo transcriptomic analysis (no reference genome available) who might give us some advice. Our main question is how to create the best set of cDNA contigs, on which we can map our RNAseq reads for the analysis of differential expression. Currently 4 larger sets of of RNAseq reads are available from different genotypes as well as draft genome assembly for one of the genotypes. We worry about the SNPs in different genotypes affecting the assembly, if we combine all the RNAseq datasets and using assemblers such as Trinity, Oases, Velvet. Might it be better to use the draft genomic assembly to obtain cDNA contigs using Tophat/cufflinks via all available RNAseq data or only using the RNAseq data from the same genotype as the genome draft? Thank you in advance Best wishes Miro Sotak ___ 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/ ___ 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/
