I can't see or access pictures in FastQC
I'm running two separate instances of Galaxy on two different servers. On both servers, whenever I run FastQC, I can see the result HTML file, but none of the pictures show up. Furthermore, if I try to access the links at the bottom of the page, they don't lead to any real files. If I look in my database/files/subfolder, I see a dataset_### file that contains the HTML info, which I am able to see in Galaxy. There is another folder named "dataset_###_files," and all of the pictures and the FastQC results zip file are contained in there. I can access them with full read permissions, and the sizes appear correct. Has anyone else experienced this problem?
Hi, Daniel. The wrapper doesn't introduce any new dependencies other than a working FastQC install in the right place so can you please let us know what happens when you run FastQC from the command line as the user running your Galaxy processes - it should start an interactive FastQC session where you can try running a real fastq input and check that you get the HTML outputs. Once it's all working from the command line, try the tool again and let us know how that turns out please? On Thu, Jun 7, 2012 at 6:58 AM, Dorset, Daniel C <daniel.dorset@vanderbilt.edu> wrote:
I’m running two separate instances of Galaxy on two different servers. On both servers, whenever I run FastQC, I can see the result HTML file, but none of the pictures show up. Furthermore, if I try to access the links at the bottom of the page, they don’t lead to any real files.
If I look in my database/files/subfolder, I see a dataset_### file that contains the HTML info, which I am able to see in Galaxy. There is another folder named “dataset_###_files,” and all of the pictures and the FastQC results zip file are contained in there. I can access them with full read permissions, and the sizes appear correct.
Has anyone else experienced this problem?
___________________________________________________________ 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:
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
Hi Ross, thanks for the reply! I ran FastQC from the command line, and it did give the proper output. Furthermore, FastQC generating the proper output when I run it from Galaxy. However, Galaxy is having trouble accessing the files. If I go into the filesystem, I can find all of the files in .../database/files/[###]/dataset_[###]_files/ I ran FastQC on the Penn State public instance, and it gives HTML output with pictures in-line and all of the linked files accessible. When I mouseover the link, it looks the same as it does on my local instances, in that the address is in the following format: [Galaxy web address]/datasets/[16 character hash]/display/[filename] Knowing what's going on "under the hood" would be extremely helpful towards my troubleshooting. So far I can't find anything interesting in paster.log, nor in the Apache log files. Thanks! Dan -----Original Message----- From: Ross [mailto:ross.lazarus@gmail.com] Sent: Wednesday, June 06, 2012 6:07 PM To: Dorset, Daniel C Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] I can't see or access pictures in FastQC Hi, Daniel. The wrapper doesn't introduce any new dependencies other than a working FastQC install in the right place so can you please let us know what happens when you run FastQC from the command line as the user running your Galaxy processes - it should start an interactive FastQC session where you can try running a real fastq input and check that you get the HTML outputs. Once it's all working from the command line, try the tool again and let us know how that turns out please? On Thu, Jun 7, 2012 at 6:58 AM, Dorset, Daniel C <daniel.dorset@vanderbilt.edu> wrote:
I'm running two separate instances of Galaxy on two different servers. On both servers, whenever I run FastQC, I can see the result HTML file, but none of the pictures show up. Furthermore, if I try to access the links at the bottom of the page, they don't lead to any real files.
If I look in my database/files/subfolder, I see a dataset_### file that contains the HTML info, which I am able to see in Galaxy. There is another folder named "dataset_###_files," and all of the pictures and the FastQC results zip file are contained in there. I can access them with full read permissions, and the sizes appear correct.
Has anyone else experienced this problem?
___________________________________________________________ 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:
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
Hi, Daniel, Sorry to say I'm unable to explain this problem with your local instance - it works fine on all of mine and on main. What do you see when you type hg tip in the root of your Galaxy clone? The current tip is hg tip changeset: 7243:37352829fedd If this is an up to date clone and you haven't made any code changes, I'm going to guess that you might have a local web server configuration issue - but maybe Nate or Dan can help? On Thu, Jun 7, 2012 at 11:54 PM, Dorset, Daniel C <daniel.dorset@vanderbilt.edu> wrote:
Hi Ross, thanks for the reply! I ran FastQC from the command line, and it did give the proper output. Furthermore, FastQC generating the proper output when I run it from Galaxy. However, Galaxy is having trouble accessing the files. If I go into the filesystem, I can find all of the files in .../database/files/[###]/dataset_[###]_files/
I ran FastQC on the Penn State public instance, and it gives HTML output with pictures in-line and all of the linked files accessible. When I mouseover the link, it looks the same as it does on my local instances, in that the address is in the following format:
[Galaxy web address]/datasets/[16 character hash]/display/[filename]
Knowing what's going on "under the hood" would be extremely helpful towards my troubleshooting. So far I can't find anything interesting in paster.log, nor in the Apache log files.
Thanks!
Dan
-----Original Message----- From: Ross [mailto:ross.lazarus@gmail.com] Sent: Wednesday, June 06, 2012 6:07 PM To: Dorset, Daniel C Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] I can't see or access pictures in FastQC
Hi, Daniel. The wrapper doesn't introduce any new dependencies other than a working FastQC install in the right place so can you please let us know what happens when you run FastQC from the command line as the user running your Galaxy processes - it should start an interactive FastQC session where you can try running a real fastq input and check that you get the HTML outputs.
Once it's all working from the command line, try the tool again and let us know how that turns out please?
On Thu, Jun 7, 2012 at 6:58 AM, Dorset, Daniel C <daniel.dorset@vanderbilt.edu> wrote:
I'm running two separate instances of Galaxy on two different servers. On both servers, whenever I run FastQC, I can see the result HTML file, but none of the pictures show up. Furthermore, if I try to access the links at the bottom of the page, they don't lead to any real files.
If I look in my database/files/subfolder, I see a dataset_### file that contains the HTML info, which I am able to see in Galaxy. There is another folder named "dataset_###_files," and all of the pictures and the FastQC results zip file are contained in there. I can access them with full read permissions, and the sizes appear correct.
Has anyone else experienced this problem?
___________________________________________________________ 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:
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
I appreciate you taking the time to help! I'm almost positive it's a local configuration issue, like you said, but without knowing how Galaxy generates or parses its internal links (in the form of [Galaxy web address]/datasets/[16 character hash]/display/[filename] ) it's tough to know how to attack the problem. I dug through some of the database tables in psql, but I couldn't find much of interest there either. hg tip result is: 7148:17d57db9a7c0 <-- that's the May 9th release Thanks again for your help! Dan
Hi, Daniel, The configuration suggested at http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy is what you followed to set your proxy up? That obfuscated link hash element is generated from internal database ids to help secure against malicious users viewing specific datasets - not something your web server configuration normally needs to know about or do anything about. The Galaxy paste process takes care of generating and interpreting them. If you want to dig deeper, the external scripting api has code for accessing datasets by generating the right hashes - see code and minimal docs at scripts/api On Fri, Jun 8, 2012 at 7:59 AM, Dorset, Daniel C <daniel.dorset@vanderbilt.edu> wrote:
I appreciate you taking the time to help! I'm almost positive it's a local configuration issue, like you said, but without knowing how Galaxy generates or parses its internal links (in the form of [Galaxy web address]/datasets/[16 character hash]/display/[filename] ) it's tough to know how to attack the problem. I dug through some of the database tables in psql, but I couldn't find much of interest there either.
hg tip result is: 7148:17d57db9a7c0 <-- that's the May 9th release
Thanks again for your help!
Dan
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
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