[galaxy-dev] IOError: [Errno 28] No space left on device
Hi all, When I added a dataset in the Manage data libraries, galaxy reported some erros. Anyone knows what's wrong? Miscellaneous information: Traceback (most recent call last): File /home/caizexi/usr/galaxy/tools/data_source/upload.py, line 384, in __main__() File /home/caizexi/usr/galaxy/tools/data_source/upload.py, line 373, in __main__ add_file( dataset, registry, js Job Standard Error Traceback (most recent call last): File /home/caizexi/usr/galaxy/tools/data_source/upload.py, line 384, in __main__() File /home/caizexi/usr/galaxy/tools/data_source/upload.py, line 373, in __main__ add_file( dataset, registry, json_file, output_path ) File /home/caizexi/usr/galaxy/tools/data_source/upload.py, line 270, in add_file line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place ) File /home/caizexi/usr/galaxy/lib/galaxy/datatypes/sniff.py, line 99, in convert_newlines fp.write( %s\n % line.rstrip( \r\n ) ) IOError: [Errno 28] No space left on device error Database/Build: ? Number of data lines: None Best regards___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] some problem with the fastq interlacer
Hi all, I ran the fastq interlacer with a fastq encoding 1.8+ data, the interlacer seems do not reganize the name of the pair-end reads, and treat the pair-end reads as non-pair-edn reads. Best regards___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Update some tools
Hi all, I need to deal with fastq encoding 1.8+ data, so I need the FASTX-Toolkit v0.0.13. So how to update the FASTX-Toolkit in the galaxy? By the way, I run a local instance of galaxy.___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] 回复： 回复： 回复： Speed up the galaxy
Hi Alex Now is an another problem. I now deal with two fastq files, there are Illumina enconding 1.8 and pair-end, so I don't need to groom. But the fact is, I need to use the filter by quality and Fastq interlacer and without groom thses two tools can not regonize the files. Any idea to solve this problem? 发件人： Bossers, Alex alex.boss...@wur.nl 收件人： 泽 蔡 caizexi...@yahoo.com.cn 抄送： galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu 发送日期： 2012年12月5日, 星期三, 4:02 上午 主题: RE: 回复： [galaxy-dev] 回复： Speed up the galaxy It seems old Illumina encoding 1.5 So yes some tools requiring the fastqsanger would need grooming. If you are up to programming you can seriously speed this up by using a precalculated transfer or hash table. That way you do not have to do any calculation but just translate each quality line using generic regexp/grep/sed like tools or $seq =~ t/STARTSCORES/SANGERSCORES/g in perl. The wiki table could be an alternative option. You still have to set the upload type to fastsanger likely since it will probably sniff the header and see its fastq but not 1.8+ encoding. Good luck! Alex Van: 泽 蔡 [caizexi...@yahoo.com.cn] Verzonden: dinsdag 4 december 2012 16:41 To: Bossers, Alex Cc: galaxy-dev@lists.bx.psu.edu Onderwerp: 回复： [galaxy-dev] 回复： Speed up the galaxy Hi Alex I look the page of wikipedia, but I have a little confused. We sequenced with solexa. I paste a read of my data, can you tell me whether I need run Groom? The read is like this:@HWUSI-EAS1734_0003_FC620JEAAXX:8:1:1174:9013#0/1 AGAAGTACATCGCGATGCCGTTNCCNNCGAAGGCGATAGNNNACAAGNCCAAATGNTTCTNCATCNNNCNCGAGNNGNCGAGGNCGCCGTGCGACCCTGC +HWUSI-EAS1734_0003_FC620JEAAXX:8:1:1174:9013#0/1 Ya^a`edddeddc\c`a`dc]\Ba^BBZ]ZZ`ZZZ]a]]BBB^[`\UB_V[V\`ZBSZX^ 发件人： Bossers, Alex alex.boss...@wur.nl 收件人： 泽 蔡 caizexi...@yahoo.com.cn 抄送： galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu; Nate Coraor n...@bx.psu.edu 发送日期： 2012年12月4日, 星期二, 下午 11:21 主题: RE: [galaxy-dev] 回复： Speed up the galaxy Hi I presume the best way to optimise your current problem is to evaluate whether you really need to groom your data!? If its old data presumably yes, but if it is recent data in Illumina 1.8+ encoding(http://en.wikipedia.org/wiki/FASTQ_format) it is not necessary speedup 100% :-) Groom would take long at our servers as well but due to the new Illumina format we didn’t bother to optimise it further by parallelisation for instance... Alex Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens ? ? Verzonden: dinsdag 4 december 2012 16:08 Aan: Nate Coraor CC: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] 回复： Speed up the galaxy Hi， I read the page of the document. But I don't think there is anything I need. Now, I installed a local instance of galaxy, and I just run it on a PC. I need to deal with large data, if I just use the default configure of galaxy, every task would take long time. For example I ran the FASTQ Groomer with a large file, the precedure is so slow, and galaxy would not use the potential of my machine. So I want to know how can I get galaxy ran faster. I already can upload files quickly and I just need to know how to ran tools quickly. 发件人： Nate Coraor n...@bx.psu.edumailto:n...@bx.psu.edu 收件人： 泽 蔡 caizexi...@yahoo.com.cnmailto:caizexi...@yahoo.com.cn 抄送： galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu 发送日期： 2012年12月4日, 星期二, 下午 9:38 主题: Re: [galaxy-dev] Speed up the galaxy On Dec 4, 2012, at 4:36 AM, 泽 蔡 wrote: Hi all, How can I speed up the galaxy? Like how to use more cores and memeries. Hi, This is a pretty broad question. However, I would recommend that you start at: http://usegalaxy.org/production --nate ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] 回复： 回复： 回复： 回复： Speed up the galaxy
Hi Brad, I'm sorry, I can not quite follow you. The pencil and the datatype tab are tools in galaxy? 发件人： Langhorst, Brad langho...@neb.com 收件人： 泽 蔡 caizexi...@yahoo.com.cn 抄送： galaxy-dev@lists.bx.psu.edu Dev galaxy-dev@lists.bx.psu.edu 发送日期： 2012年12月7日, 星期五, 7:53 下午 主题: Re: [galaxy-dev] 回复： 回复： 回复： Speed up the galaxy You can just change the format of the data from fastq to fastqsanger if you're sure about the error format (use the pencil, then datatype tab) note: fastqsanger !=fastqcsanger Brad On Dec 7, 2012, at 3:20 AM, 泽 蔡 caizexi...@yahoo.com.cn wrote: Hi Alex Now is an another problem. I now deal with two fastq files, there are Illumina enconding 1.8 and pair-end, so I don't need to groom. But the fact is, I need to use the filter by quality and Fastq interlacer and without groom thses two tools can not regonize the files. Any idea to solve this problem? 发件人： Bossers, Alex alex.boss...@wur.nl 收件人： 泽 蔡 caizexi...@yahoo.com.cn 抄送： galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu 发送日期： 2012年12月5日, 星期三, 4:02 上午 主题: RE: 回复： [galaxy-dev] 回复： Speed up the galaxy It seems old Illumina encoding 1.5 So yes some tools requiring the fastqsanger would need grooming. If you are up to programming you can seriously speed this up by using a precalculated transfer or hash table. That way you do not have to do any calculation but just translate each quality line using generic regexp/grep/sed like tools or $seq =~ t/STARTSCORES/SANGERSCORES/g in perl. The wiki table could be an alternative option. You still have to set the upload type to fastsanger likely since it will probably sniff the header and see its fastq but not 1.8+ encoding. Good luck! Alex Van: 泽 蔡 [caizexi...@yahoo.com.cn] Verzonden: dinsdag 4 december 2012 16:41 To: Bossers, Alex Cc: mailto:galaxy-dev@lists.bx.psu.edu Onderwerp: 回复： [galaxy-dev] 回复： Speed up the galaxy Hi Alex I look the page of wikipedia, but I have a little confused. We sequenced with solexa. I paste a read of my data, can you tell me whether I need run Groom? The read is like this:@HWUSI-EAS1734_0003_FC620JEAAXX:8:1:1174:9013#0/1 AGAAGTACATCGCGATGCCGTTNCCNNCGAAGGCGATAGNNNACAAGNCCAAATGNTTCTNCATCNNNCNCGAGNNGNCGAGGNCGCCGTGCGACCCTGC +HWUSI-EAS1734_0003_FC620JEAAXX:8:1:1174:9013#0/1 Ya^a`edddeddc\c`a`dc]\Ba^BBZ]ZZ`ZZZ]a]]BBB^[`\UB_V[V\`ZBSZX^ 发件人： Bossers, Alex alex.boss...@wur.nl 收件人： 泽 蔡 caizexi...@yahoo.com.cn 抄送： galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu; Nate Coraor n...@bx.psu.edu 发送日期： 2012年12月4日, 星期二, 下午 11:21 主题: RE: [galaxy-dev] 回复： Speed up the galaxy Hi I presume the best way to optimise your current problem is to evaluate whether you really need to groom your data!? If its old data presumably yes, but if it is recent data in Illumina 1.8+ encoding(http://en.wikipedia.org/wiki/FASTQ_format) it is not necessary speedup 100% :-) Groom would take long at our servers as well but due to the new Illumina format we didn’t bother to optimise it further by parallelisation for instance... Alex Van: mailto:galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens ? ? Verzonden: dinsdag 4 december 2012 16:08 Aan: Nate Coraor CC: mailto:galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] 回复： Speed up the galaxy Hi， I read the page of the document. But I don't think there is anything I need. Now, I installed a local instance of galaxy, and I just run it on a PC. I need to deal with large data, if I just use the default configure of galaxy, every task would take long time. For example I ran the FASTQ Groomer with a large file, the precedure is so slow, and galaxy would not use the potential of my machine. So I want to know how can I get galaxy ran faster. I already can upload files quickly and I just need to know how to ran tools quickly. 发件人： Nate Coraor n...@bx.psu.edumailto:n...@bx.psu.edu 收件人： 泽 蔡 caizexi...@yahoo.com.cnmailto:caizexi...@yahoo.com.cn 抄送： galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu galaxy-...@bx.psu.edumailto:galaxy-...@bx.psu.edu 发送日期： 2012年12月4日, 星期二, 下午 9:38 主题: Re: [galaxy-dev] Speed up the galaxy On Dec 4, 2012, at 4:36 AM, 泽 蔡 wrote: Hi all, How can I speed up the galaxy? Like how to use more cores and memeries. Hi, This is a pretty broad question. However, I would recommend that you start at: http://usegalaxy.org/production --nate ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions
[galaxy-dev] 回复： 回复： Speed up the galaxy
Hi Alex I look the page of wikipedia, but I have a little confused. We sequenced with solexa. I paste a read of my data, can you tell me whether I need run Groom? The read is like this:@HWUSI-EAS1734_0003_FC620JEAAXX:8:1:1174:9013#0/1 AGAAGTACATCGCGATGCCGTTNCCNNCGAAGGCGATAGNNNACAAGNCCAAATGNTTCTNCATCNNNCNCGAGNNGNCGAGGNCGCCGTGCGACCCTGC +HWUSI-EAS1734_0003_FC620JEAAXX:8:1:1174:9013#0/1 Ya^a`edddeddc\c`a`dc]\Ba^BBZ]ZZ`ZZZ]a]]BBB^[`\UB_V[V\`ZBSZX^ 发件人： Bossers, Alex alex.boss...@wur.nl 收件人： 泽 蔡 caizexi...@yahoo.com.cn 抄送： galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu; Nate Coraor n...@bx.psu.edu 发送日期： 2012年12月4日, 星期二, 下午 11:21 主题: RE: [galaxy-dev] 回复： Speed up the galaxy Hi I presume the best way to optimise your current problem is to evaluate whether you really need to groom your data!? If its old data presumably yes, but if it is recent data in Illumina 1.8+ encoding(http://en.wikipedia.org/wiki/FASTQ_format) it is not necessary speedup 100% :-) Groom would take long at our servers as well but due to the new Illumina format we didn’t bother to optimise it further by parallelisation for instance... Alex Van:galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens ? ? Verzonden: dinsdag 4 december 2012 16:08 Aan: Nate Coraor CC: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] 回复：Speed up the galaxy Hi， I read the page of the document. But I don't think there is anything I need. Now, I installed a local instance of galaxy, and I just run it on a PC. I need to deal with large data, if I just use the default configure of galaxy, every task would take long time. For example I ran the FASTQ Groomer with a large file, the precedure is so slow, and galaxy would not use the potential of my machine. So I want to know how can I get galaxy ran faster. I already can upload files quickly and I just need to know how to ran tools quickly. 发件人：Nate Coraor n...@bx.psu.edu 收件人：泽蔡caizexi...@yahoo.com.cn 抄送：galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu 发送日期：2012年12月4日, 星期二, 下午9:38 主题:Re: [galaxy-dev] Speed up the galaxy On Dec 4, 2012, at 4:36 AM, 泽蔡wrote: Hi all, How can I speed up the galaxy? Like how to use more cores and memeries. Hi, This is a pretty broad question. However, I would recommend that you start at: http://usegalaxy.org/production --nate ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Galaxy admin users
Hi all, I install a local instance on a linux system. And I tried to use the admin features of Galaxy, so I add my Galaxy login ( email ) to the list in the following config setting in the Galaxy configuration file universe_wsgi.ini. # this should be a comma-separated list of valid Galaxy users admin_users = @(the email I registered) But when I login, I did not see the Admin menu item on the top Galaxy menu bar. Why? Should I change anything esle?___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] The qiuck way to upload large file
Hi all, I'm a new guy of galaxy and bioinformatics. I read the document of galaxy, but it's so hard to find what I need. I already set up a locale instance of galaxy, it works fine. The problem is I need to analysis large data, but the upload file is so slow, is there some ways I can upload large file quickly?___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
