Hi Jen, I'd also like to be able to reload *.loc files without having to restart Galaxy. I filed an enhancement bug: https://bitbucket.org/galaxy/galaxy-central/issue/538 Peter On Wed, Apr 20, 2011 at 9:18 PM, Jennifer Jackson <jen@bx.psu.edu> wrote:

Hello Luobin,

At this time, a restart is necessary for the dataset to be incorporated.

Thanks for using Galaxy!

Best,

Jen Galaxy team

On 4/12/11 1:50 PM, Luobin Yang wrote:

...

Hi all,

I am wondering if it's possible to to reload a ".loc" file without restarting the Galaxy server?

Thanks, Luobin

Hello Curtis, The coordinates of your match are with respect to the fasta sequence, not with respect to the reference genome. Only data mapped to the reference genome can be viewed in the UCSC Browser You will need to calculate from the position of the match in the fasta sequence back through to the reference genome. One suggested way to do this: a) Merge together the original genomic coordinates of the 2kb regions with each line of output from fuzznuc. Use the original source fasta sequence name as the common key for the merge. If both data are in BED format, that would be ideal and make the following steps possible. You may need to split the file based on whether the original fasta sequence came from the positive or negative strand to run "b" and "c" below separately. b) Use "Text Manipulation -> Compute an expression on every row" to create new coordinates. For example, if your data is on the positive strand, and base 1 in your fasta file was genomic coordinate 100, and the alignment from fuzznuc started at base 5 (local coordinate == "4" if in BED format with a zero-based start), then the new genomic start coordinate would be [100 + 4)] = 104. Do this for both start and stop. c) Adjust the logic for "b" if any of your original fasta sequences are from the negative strand, on the negative strand portion of your data ("b" would be run on just the positive strand portion of your data). d) arrange/cut the resulting file down into a standard BED format to remove the local coordinates and keep the genomic coordinates, using the original chromosome names. e) once the logic for the calculations is worked out, save the process into a workflow for use again. Hopefully this helps, Best, Jen Galaxy team On 5/13/11 9:32 AM, Robert Curtis Hendrickson wrote:

Folks,

I wanted to scan the 2kb upstream of a list of human gene isoforms for TFBS using fuzznuc. I was able to "Get Data"> "UCSC Main"> "As sequence" and get my sequences "EMBOSS"> fuzznuc ran fine, and output the hits

HOWEVER, fuzznuc lost the genomic position information that UCSC has put after a space in the sequence headers of the FASTA file. It only provided offsets within the fasta.

http://main.g2.bx.psu.edu/u/curtish-uab/h/ucsc-fuzznuc-ucsc-broken

Thus, when I converted the fuzznuc output back to a BED file and tried to visualize the hits in UCSC browser, it failed with "invalid BED File". I tried fuzznuc with output: seqtable, feattable and gff3, but in all cases the genomic position was missing, and being a bit of Galaxy novice, I couldn't figure out how to get the output back to UCSC to visualize the hits.

Can anyone tell me how to link up these tools correctly, or share a history with some other tool set that accomplishes this goal?

Regards, Curtis

Research Associate Center for Clinical and Translational Science University of Alabama at Birmingham

___________________________________________________________ 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:

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-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

Hello Curtis, No need to use the fasta headers from your original fasta file. To obtain the coordinates in BED format: using "Get Data -> UCSC main" again to link to the UCSC Table browser, set the same selection criteria as for the original fasta sequence, only change the output type to be "BED" (instead of "sequence"). Once in your Galaxy history, this format will be easier to work with. Best, Jen Galaxy team On 5/16/11 9:04 PM, Robert Curtis Hendrickson wrote:

Jennifer,

Thanks for the outline. I'll try that approach.

However, it seems rather painful to have to join the fuzznuc output back to the original fasta to get at the header information that really should have been passed along. It would see that there must be a way to get the data out of UCSC without that space in the fasta header, so that the chromosome& genomic location get correctly preserved in the fuzznuc output. Failing that, is there an easy text manipulation that would convert that fasta header space to a "|"?

Regards, Curtis

-----Original Message----- From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Monday, May 16, 2011 6:50 PM To: Robert Curtis Hendrickson Cc: 'galaxy-user@lists.bx.psu.edu' Subject: Re: [galaxy-user] UCSC->EMBOSS/fuzznuc->UCSC workflow?

Hello Curtis,

The coordinates of your match are with respect to the fasta sequence, not with respect to the reference genome. Only data mapped to the reference genome can be viewed in the UCSC Browser

You will need to calculate from the position of the match in the fasta sequence back through to the reference genome.

One suggested way to do this:

a) Merge together the original genomic coordinates of the 2kb regions with each line of output from fuzznuc. Use the original source fasta sequence name as the common key for the merge. If both data are in BED format, that would be ideal and make the following steps possible. You may need to split the file based on whether the original fasta sequence came from the positive or negative strand to run "b" and "c" below separately. b) Use "Text Manipulation -> Compute an expression on every row" to create new coordinates. For example, if your data is on the positive strand, and base 1 in your fasta file was genomic coordinate 100, and the alignment from fuzznuc started at base 5 (local coordinate == "4" if in BED format with a zero-based start), then the new genomic start coordinate would be [100 + 4)] = 104. Do this for both start and stop. c) Adjust the logic for "b" if any of your original fasta sequences are from the negative strand, on the negative strand portion of your data ("b" would be run on just the positive strand portion of your data). d) arrange/cut the resulting file down into a standard BED format to remove the local coordinates and keep the genomic coordinates, using the original chromosome names. e) once the logic for the calculations is worked out, save the process into a workflow for use again.

Hopefully this helps,

Best,

Jen Galaxy team

On 5/13/11 9:32 AM, Robert Curtis Hendrickson wrote:

...

Folks,

I wanted to scan the 2kb upstream of a list of human gene isoforms for TFBS using fuzznuc. I was able to "Get Data"> "UCSC Main"> "As sequence" and get my sequences "EMBOSS"> fuzznuc ran fine, and output the hits

HOWEVER, fuzznuc lost the genomic position information that UCSC has put after a space in the sequence headers of the FASTA file. It only provided offsets within the fasta.

http://main.g2.bx.psu.edu/u/curtish-uab/h/ucsc-fuzznuc-ucsc-broken

Thus, when I converted the fuzznuc output back to a BED file and tried to visualize the hits in UCSC browser, it failed with "invalid BED File". I tried fuzznuc with output: seqtable, feattable and gff3, but in all cases the genomic position was missing, and being a bit of Galaxy novice, I couldn't figure out how to get the output back to UCSC to visualize the hits.

Can anyone tell me how to link up these tools correctly, or share a history with some other tool set that accomplishes this goal?

Regards, Curtis

Research Associate Center for Clinical and Translational Science University of Alabama at Birmingham

___________________________________________________________ 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/

-- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

Roman Valls wrote:

On standard UNIX, the SIGHUP signal (kill -HUP <PID>) is used to perform this kind of actions (re-read config files) on almost all daemons [1].

Doing a quick grep:

$ grep -ri "HUP" galaxy-central

Nothing shows up, so as Jen indicated, does not seem to be implemented at first glance... but one could have a look at:

http://docs.python.org/library/signal.html

And handle that signal... I guess that the daemon would be "paster", but haven't found where it reads the loc files :-S

I actually implemented SIGHUP and then found that it would not work: http://bugs.python.org/issue7978 If that patch actually made it to a 2.6 minor release it may solve the problem and I could commit this code. --nate

[1] http://en.wikipedia.org/wiki/SIGHUP

On 2011-04-12 22:50, Luobin Yang wrote:

...

Hi all,

I am wondering if it's possible to to reload a ".loc" file without restarting the Galaxy server?

Thanks, Luobin

___________________________________________________________ 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/

---

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/