December 2012 - galaxy-dev - lists.galaxyproject.org

Error in TopHat
by Sachit Adhikari 19 Dec '12

19 Dec '12

This is the error I am getting while running Tophat. What's causing this? I have the default hg19 index files. Error in tophat: [Tue Dec 18 10:08:33 2012] Beginning TopHat run (v1.3.3) ----------------------------------------------- [Tue Dec 18 10:08:33 2012] Preparing output location ./tophat_out/ [Tue Dec 18 10:08:33 2012] Checking for Bowtie index files Error: Could not find Bowtie index files /opt/galaxyprod/galaxy-dist/data/hg19/hg19,/data/bowtie2-2.0.2/hg19.* TopHat v1.3.3 TopHat v1.3.3 tophat -p 4 /opt/galaxyprod/galaxy-dist/data/hg19/hg19,/data/bowtie2-2.0.2/hg19 /opt/galaxyprod/galaxy-dist/database/files/000/dataset_45.dat

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producing HTML output with images
by Nikhil Joshi 19 Dec '12

19 Dec '12

Hi all, I am having trouble producing HTML output with images. In the past I have been able to produce HTML files with no images and it seemed to work fine. However, now I am writing a script that produces diagnostic images and I want to display all of the images on one page using HTML. I am using the "files_path" variable to create the plots in the working directory, and then I am using the "extra_files_path" variable to access the final plot from the html file. I look at the resulting HTML files and it points to the proper plot full path, and the plot DOES exist... but when I click to view the output, the plot doesn't render. It just shows an empty box with a "broken image" icon, however, the text does render. I copy the plot file, and I can view it fine by itself. I copy the plot and the html and I can view the page just fine offline, but galaxy doesn't want to render the image for some reason. What am I doing wrong? - Nik. -- Nikhil Joshi Bioinformatics Programmer UC Davis Genome Center Davis, CA

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How to refresh static/welcome.html
by greg 19 Dec '12

19 Dec '12

Hi guys, When I make a change to welcome.html how do I get galaxy to start displaying the new version? Thanks, Greg

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Re: [galaxy-dev] 回复： IOError: [Errno 28] No space left on device
by Ross 19 Dec '12

19 Dec '12

Looks to me like tmpfs is full and maybe too small. http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster?highlight=%2… suggests setting $TEMP= somewhere sensible. But that's not always enough depending on the third party executables you're running so you might want a bigger /tmpfs too. On Wed, Dec 19, 2012 at 6:52 PM, 泽蔡 <caizexi123(a)yahoo.com.cn> wrote: > Hi Ross, > > Filesystem 1K-blocks Used Available Use% Mounted on > /dev/sda1 90717816 89796388 0 100% / > tmpfs 66070064 372 66069692 1% /dev/shm > /dev/sdb1 1968618280 199800 1868418484 1% /copy > /dev/sdb2 7336174008 3759366732 3204151100 54% /home > > Then how shall I do? > > Best regard! > > *发件人：* Ross <ross.lazarus(a)gmail.com> > *收件人：* 泽蔡 <caizexi123(a)yahoo.com.cn> > *发送日期：* 2012年12月19日, 星期三, 2:30 下午 > *主题:* Re: [galaxy-dev] IOError: [Errno 28] No space left on device > > Possibly not enough space left on the volume being used for temporary > files. > > What does > df > show? > > > > On Wed, Dec 19, 2012 at 4:42 PM, 泽蔡 <caizexi123(a)yahoo.com.cn> wrote: > > 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 > > > >

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IOError: [Errno 28] No space left on device
by 泽蔡 19 Dec '12

19 Dec '12

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

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MACS not found
by Alfonso Garrido-Lecca 19 Dec '12

19 Dec '12

Hello, I am new in using galaxy on the cloud. I am trying to analyze my ChIP-seq data. However, when I try to run the MACS peak calling algorithm on my BAM files I get an error message saying "MACS: not found". Any ideas? thanks!

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Re: [galaxy-dev] Galaxy users on virtual machine
by Oleksandr Moskalenko 18 Dec '12

18 Dec '12

We're using ldap authentication on our cluster, so our /etc/passwd files don't have any user data and the credentials are returned by ldap. You will have to adjust this to your situation. You can rsync /etc/passwd from elsewhere or fiddle with PAM to work something out for your key-based setup. Sorry, I don't have more insight into that part. Regards, Alex On Dec 18, 2012, at 2:27 PM, cganote(a)iu.edu wrote: > Hi Alex, > > I see what you are saying, but I think our situations are slightly different. > The line > self.__user_system_pwent = pwd.getpwnam(job.user.email.split('@')[0] ) > *does* return the correct username, however, that user is not present in the Virtual machine that is running Galaxy, so when the job runner calls for pwd.getpwuid(), there is nothing there. By the way, the VM uses key authentication only, not passwords. > > The problem I think I'm having is that the /etc/passwd file I want to use is located on the cluster, not on the virtual machine. I'm not sure if I can just copy that file over. How else can I get ahold of the uid of the user who cannot log in to the machine Galaxy is running on? > > Thanks for the help, > > Carrie Ganote

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Re: [galaxy-dev] Galaxy users on virtual machine
by Ganote, Carrie L 18 Dec '12

18 Dec '12

Hi Alex, I see what you are saying, but I think our situations are slightly different. The line self.__user_system_pwent = pwd.getpwnam(job.user.email.split('@')[0] ) *does* return the correct username, however, that user is not present in the Virtual machine that is running Galaxy, so when the job runner calls for pwd.getpwuid(), there is nothing there. By the way, the VM uses key authentication only, not passwords. The problem I think I'm having is that the /etc/passwd file I want to use is located on the cluster, not on the virtual machine. I'm not sure if I can just copy that file over. How else can I get ahold of the uid of the user who cannot log in to the machine Galaxy is running on? Thanks for the help, Carrie Ganote __________________________________________________________________________________ Hi Carrie, I run a crontab job every 5 minutes that repopulates the galaxy database with the real user names we use instead of the email style user names by updating the galaxy_user.username column. Then, I patch jobs/__init__.py as follows: # self.__user_system_pwent = pwd.getpwnam( job.user.email.split('@')[0] ) self.__user_system_pwent = pwd.getpwnam( job.user.username ) Regards, Alex

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Working with compressed files
by Fenglou Mao 18 Dec '12

18 Dec '12

Is Galaxy capable of working with compressed files such as *.fastq.gz? Thanks, Fenglou

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question of galaxy on cloud
by Sun, Wenping [USA] 18 Dec '12

18 Dec '12

Dear Galaxy members, I am new to galaxy and just installed galaxy on aws cloud. I am testing how it works and have the following question below: 1. If I upload dataset with url, where the data location after uploading? 2. How many Gb space from root of instance would be more efficient to run galaxy? If root space does not matter, what else would affect the overall performance? 3. I tried to test bowtie2 with the dataset I uploaded, however, the window for reference genome is very narrow and nothing can be selected. When I omit that option to execute bowtie2, galaxy give error message for requesting reference genome. I am using hg19, should I upload myself? 4. Same error happen for me to run fastqc --- the reference genome selection window is way too narrow and nothing can be selected I really appreciate your inputs and helps! Kind regards, Kathryn

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