Hello all, Has anyone done a wrapper for HMMER2 or HMMER3? http://hmmer.janelia.org/software I can't find anything in the Tool Shed http://toolshed.g2.bx.psu.edu/ so we are likely to look into doing this ourselves - starting with hmmerscan. Thanks, Peter
Hi Peter, I think hmmerscan has been wrapped, but there is a missing "e" in the repository name. Look for "hmmscan" in the toolshed. The description for it is: hmmscan, for searching pfam with AA seqs. also included is hmm datatypes although hmmbuild, etc. isnt included yetX ill try to finish the rest of the hmmer suite soon Does that help? Dave C. On Tue, Feb 28, 2012 at 2:31 AM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
Hello all,
Has anyone done a wrapper for HMMER2 or HMMER3? http://hmmer.janelia.org/software
I can't find anything in the Tool Shed http://toolshed.g2.bx.psu.edu/ so we are likely to look into doing this ourselves - starting with hmmerscan.
Thanks,
Peter ___________________________________________________________ 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:
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On Tue, Feb 28, 2012 at 10:31 PM, Dave Clements <clements@galaxyproject.org> wrote:
Hi Peter,
I think hmmerscan has been wrapped, but there is a missing "e" in the repository name. Look for "hmmscan" in the toolshed. The description for it is:
hmmscan, for searching pfam with AA seqs. also included is hmm datatypes although hmmbuild, etc. isnt included yetX ill try to finish the rest of the hmmer suite soon
Does that help?
Dave C.
Very helpful Dave, thanks. Actually hmmscan is the name of one of the HMMER binaries, rather than hmmerscan (with an 'er' in the middle, which was a typo on my part). I've included Edward directly in this thread hoping he can clarify which version of HMMER he was wrapping (2 vs 3). Also I'd like to ask Edward if he could add the word HMMER to the tool's description to facilitate future searchers (and HMMER2 or HMMER3 as appropriate). I might be interested in helping to extend the wrapper for more of the HMMER3 toolkit. In particular hmmsearch might be relevant, which is designed for one (or a few) profiles vs. a big seq database while hmmscan is designed for one (or a few) sequences vs. a big profile database. See http://selab.janelia.org/people/eddys/blog/?p=424 Regards, Peter
hi, peter - i will fix the description and upload hmmsearch and infernal today. On Wed, Feb 29, 2012 at 2:05 AM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
Hi Peter,
I think hmmerscan has been wrapped, but there is a missing "e" in the repository name. Look for "hmmscan" in the toolshed. The description for it is:
hmmscan, for searching pfam with AA seqs. also included is hmm datatypes although hmmbuild, etc. isnt included yetX ill try to finish the rest of
On Tue, Feb 28, 2012 at 10:31 PM, Dave Clements <clements@galaxyproject.org> wrote: the
hmmer suite soon
Does that help?
Dave C.
Very helpful Dave, thanks.
Actually hmmscan is the name of one of the HMMER binaries, rather than hmmerscan (with an 'er' in the middle, which was a typo on my part).
I've included Edward directly in this thread hoping he can clarify which version of HMMER he was wrapping (2 vs 3).
Also I'd like to ask Edward if he could add the word HMMER to the tool's description to facilitate future searchers (and HMMER2 or HMMER3 as appropriate).
I might be interested in helping to extend the wrapper for more of the HMMER3 toolkit. In particular hmmsearch might be relevant, which is designed for one (or a few) profiles vs. a big seq database while hmmscan is designed for one (or a few) sequences vs. a big profile database. See http://selab.janelia.org/people/eddys/blog/?p=424
Regards,
Peter
On Wed, Feb 29, 2012 at 5:56 PM, Edward Kirton <eskirton@lbl.gov> wrote:
hi, peter - i will fix the description and upload hmmsearch and infernal today.
Great. Assuming hmmscan and hmmsearch have (almost) the same command line API, there is something to be said for presenting them as one tool in Galaxy, with a drop down selection between them (with help text about which is recommend adapted from the HMMER blog post). One could even have an automatic selection by a wrapper script based on the number of query sequences and the number of HMMs. My thinking here is the detail of hmmscan vs hmmsearch is purely an implementation detail that the end user shouldn't have to worry about. Or just duplicate most of the XML code and have two wrappers. But as far as I know there isn't (yet) a nice way of reusing XML snippets between tool wrappers... which would be handy. Thanks, Peter
great suggestion; i'll make those changes On Wed, Feb 29, 2012 at 10:05 AM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
On Wed, Feb 29, 2012 at 5:56 PM, Edward Kirton <eskirton@lbl.gov> wrote:
hi, peter - i will fix the description and upload hmmsearch and infernal today.
Great.
Assuming hmmscan and hmmsearch have (almost) the same command line API, there is something to be said for presenting them as one tool in Galaxy, with a drop down selection between them (with help text about which is recommend adapted from the HMMER blog post). One could even have an automatic selection by a wrapper script based on the number of query sequences and the number of HMMs. My thinking here is the detail of hmmscan vs hmmsearch is purely an implementation detail that the end user shouldn't have to worry about.
Or just duplicate most of the XML code and have two wrappers. But as far as I know there isn't (yet) a nice way of reusing XML snippets between tool wrappers... which would be handy.
Thanks,
Peter
i created a new toolshed repo, hmmer since i couldn't rename it. as suggested, it has the hmmscan/hmmsearch as one tool, plus hmmpress. will add hmmbuild, hmmalign asap; others upon request. dave, is there a way to delete an old tool? (hmmscan) On Wed, Feb 29, 2012 at 10:12 AM, Edward Kirton <eskirton@lbl.gov> wrote:
great suggestion; i'll make those changes
On Wed, Feb 29, 2012 at 10:05 AM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
On Wed, Feb 29, 2012 at 5:56 PM, Edward Kirton <eskirton@lbl.gov> wrote:
hi, peter - i will fix the description and upload hmmsearch and infernal today.
Great.
Assuming hmmscan and hmmsearch have (almost) the same command line API, there is something to be said for presenting them as one tool in Galaxy, with a drop down selection between them (with help text about which is recommend adapted from the HMMER blog post). One could even have an automatic selection by a wrapper script based on the number of query sequences and the number of HMMs. My thinking here is the detail of hmmscan vs hmmsearch is purely an implementation detail that the end user shouldn't have to worry about.
Or just duplicate most of the XML code and have two wrappers. But as far as I know there isn't (yet) a nice way of reusing XML snippets between tool wrappers... which would be handy.
Thanks,
Peter
Hi Ed, Do you want the hmmscan repository itself deleted? It's been downloaded / cloned 86 times, although it is never been automatically installed into a local Galaxy since the contained tool does not properly load into Galaxy. We generally do not like to delete things like this because doing do prevents reproducibility. I'm looking for feedback from the community on this one - does eliminating this repository affect anyone? Thanks for the new contributions tot he tool shed! Greg Von Kuster On Mar 6, 2012, at 1:47 AM, Edward Kirton wrote:
i created a new toolshed repo, hmmer since i couldn't rename it. as suggested, it has the hmmscan/hmmsearch as one tool, plus hmmpress. will add hmmbuild, hmmalign asap; others upon request.
dave, is there a way to delete an old tool? (hmmscan)
On Wed, Feb 29, 2012 at 10:12 AM, Edward Kirton <eskirton@lbl.gov> wrote: great suggestion; i'll make those changes
On Wed, Feb 29, 2012 at 10:05 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote: On Wed, Feb 29, 2012 at 5:56 PM, Edward Kirton <eskirton@lbl.gov> wrote:
hi, peter - i will fix the description and upload hmmsearch and infernal today.
Great.
Assuming hmmscan and hmmsearch have (almost) the same command line API, there is something to be said for presenting them as one tool in Galaxy, with a drop down selection between them (with help text about which is recommend adapted from the HMMER blog post). One could even have an automatic selection by a wrapper script based on the number of query sequences and the number of HMMs. My thinking here is the detail of hmmscan vs hmmsearch is purely an implementation detail that the end user shouldn't have to worry about.
Or just duplicate most of the XML code and have two wrappers. But as far as I know there isn't (yet) a nice way of reusing XML snippets between tool wrappers... which would be handy.
Thanks,
Peter
___________________________________________________________ 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:
i gave it a bad name previously and peter didn't find it in a search at first, but i couldn't change the name, so i created a new repository. i put a note in the old repo (hmmscan), referring to the new repo (hmmer). that may suffice. however you folks how you want to handle it is fine. On Tue, Mar 6, 2012 at 3:38 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Ed,
Do you want the hmmscan repository itself deleted? It's been downloaded / cloned 86 times, although it is never been automatically installed into a local Galaxy since the contained tool does not properly load into Galaxy. We generally do not like to delete things like this because doing do prevents reproducibility. I'm looking for feedback from the community on this one - does eliminating this repository affect anyone?
Thanks for the new contributions tot he tool shed!
Greg Von Kuster
On Mar 6, 2012, at 1:47 AM, Edward Kirton wrote:
i created a new toolshed repo, hmmer since i couldn't rename it. as suggested, it has the hmmscan/hmmsearch as one tool, plus hmmpress. will add hmmbuild, hmmalign asap; others upon request.
dave, is there a way to delete an old tool? (hmmscan)
On Wed, Feb 29, 2012 at 10:12 AM, Edward Kirton <eskirton@lbl.gov> wrote:
great suggestion; i'll make those changes
On Wed, Feb 29, 2012 at 10:05 AM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
On Wed, Feb 29, 2012 at 5:56 PM, Edward Kirton <eskirton@lbl.gov> wrote:
hi, peter - i will fix the description and upload hmmsearch and infernal today.
Great.
Assuming hmmscan and hmmsearch have (almost) the same command line API, there is something to be said for presenting them as one tool in Galaxy, with a drop down selection between them (with help text about which is recommend adapted from the HMMER blog post). One could even have an automatic selection by a wrapper script based on the number of query sequences and the number of HMMs. My thinking here is the detail of hmmscan vs hmmsearch is purely an implementation detail that the end user shouldn't have to worry about.
Or just duplicate most of the XML code and have two wrappers. But as far as I know there isn't (yet) a nice way of reusing XML snippets between tool wrappers... which would be handy.
Thanks,
Peter
___________________________________________________________ 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:
On Tuesday, March 6, 2012, Edward Kirton <eskirton@lbl.gov> wrote:
i gave it a bad name previously and peter didn't find it in a search at first, but i couldn't change the name, so i created a new repository. i put a note in the old repo (hmmscan), referring to the new repo (hmmer). that may suffice. however you folks how you want to handle it is fine.
Surely once the description was updated a search on hmmer would find the old repository? Well anyway, now there are two there should be a way to hide or deprecate one. On a related note, I have a couple of old tools in the ToolShed which I have just labeled as deprecated in the description (and if memory serves, marked as hidden in the XML, so existing workflows and history's can still run the tool, but no new usage should be possible). Peter
Edward, I've marked your hmmscan repository as deleted so it will not longer be displayed. I can undelete it if requested by anyone. Peter, I've left your deprecated repositories alone, so they are still accessible. I'll mark them deleted as well if you want. On Mar 6, 2012, at 3:37 PM, Edward Kirton wrote:
i gave it a bad name previously and peter didn't find it in a search at first, but i couldn't change the name, so i created a new repository. i put a note in the old repo (hmmscan), referring to the new repo (hmmer). that may suffice. however you folks how you want to handle it is fine.
On Tue, Mar 6, 2012 at 3:38 AM, Greg Von Kuster <greg@bx.psu.edu> wrote: Hi Ed,
Do you want the hmmscan repository itself deleted? It's been downloaded / cloned 86 times, although it is never been automatically installed into a local Galaxy since the contained tool does not properly load into Galaxy. We generally do not like to delete things like this because doing do prevents reproducibility. I'm looking for feedback from the community on this one - does eliminating this repository affect anyone?
Thanks for the new contributions tot he tool shed!
Greg Von Kuster
On Mar 6, 2012, at 1:47 AM, Edward Kirton wrote:
i created a new toolshed repo, hmmer since i couldn't rename it. as suggested, it has the hmmscan/hmmsearch as one tool, plus hmmpress. will add hmmbuild, hmmalign asap; others upon request.
dave, is there a way to delete an old tool? (hmmscan)
On Wed, Feb 29, 2012 at 10:12 AM, Edward Kirton <eskirton@lbl.gov> wrote: great suggestion; i'll make those changes
On Wed, Feb 29, 2012 at 10:05 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote: On Wed, Feb 29, 2012 at 5:56 PM, Edward Kirton <eskirton@lbl.gov> wrote:
hi, peter - i will fix the description and upload hmmsearch and infernal today.
Great.
Assuming hmmscan and hmmsearch have (almost) the same command line API, there is something to be said for presenting them as one tool in Galaxy, with a drop down selection between them (with help text about which is recommend adapted from the HMMER blog post). One could even have an automatic selection by a wrapper script based on the number of query sequences and the number of HMMs. My thinking here is the detail of hmmscan vs hmmsearch is purely an implementation detail that the end user shouldn't have to worry about.
Or just duplicate most of the XML code and have two wrappers. But as far as I know there isn't (yet) a nice way of reusing XML snippets between tool wrappers... which would be handy.
Thanks,
Peter
___________________________________________________________ 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:
On Wed, Feb 29, 2012 at 6:12 PM, Edward Kirton <eskirton@lbl.gov> wrote:
great suggestion; i'll make those changes
Hi Edward, It has taken me a while but I'm how trying to use HMMER3, and do so from within Galaxy. I've realised that the per sequence and per domain tables from hmmscan and hmmsearch (via the --tblout and --domtblout switches) are NOT tab separated, but space separated to give an eye pleasing column based layout. However, your wrapper tells Galaxy they are "tabular". As a result, Galaxy treats them like tables with one column, which means all the table operations like filtering on a particular column are not possible. Has this not affected your users? I ran into some similar problems wrapping other tools giving table based output, and used a wrapper script to make them into tab separated tables for use in Galaxy. e.g. SignalP 3 (spaces), EffectiveT4 (semi-colons). Would you agree that a wrapper script to reformat the HMMER3 tables into tab-separated tables would be the best solution? Would you accept a code contribution to do this? Regards, Peter
On Fri, May 25, 2012 at 4:54 PM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
I ran into some similar problems wrapping other tools giving table based output, and used a wrapper script to make them into tab separated tables for use in Galaxy. e.g. SignalP 3 (spaces), EffectiveT4 (semi-colons).
Sorry, that was a typo for EffectiveT3 from http://effectors.org/ (my wrapper is on the Tool Shed). Peter
On Fri, May 25, 2012 at 4:54 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Edward,
It has taken me a while but I'm how trying to use HMMER3, and do so from within Galaxy.
I've realised that the per sequence and per domain tables from hmmscan and hmmsearch (via the --tblout and --domtblout switches) are NOT tab separated, but space separated to give an eye pleasing column based layout.
However, your wrapper tells Galaxy they are "tabular". As a result, Galaxy treats them like tables with one column, which means all the table operations like filtering on a particular column are not possible. Has this not affected your users?
I ran into some similar problems wrapping other tools giving table based output, and used a wrapper script to make them into tab separated tables for use in Galaxy. e.g. SignalP 3 (spaces), EffectiveT3 (semi-colons).
Would you agree that a wrapper script to reformat the HMMER3 tables into tab-separated tables would be the best solution? Would you accept a code contribution to do this?
Regards,
Peter
Hi Edward, I've written a simple HMMER3 table to tabular script in Python, https://github.com/peterjc/picobio/blob/master/hmmer/hmmer_table2tabular.py Would you prefer to: (a) amend the XML to call HMMER, and then call the conversion script twice. (b) turn this into a single wrapper script which calls HMMER3 and then converts the two tables (using a multiple command line call with shell semi-colon separators). (c) do something else? I favour the wrapper script option as more flexible in the long run (e.g. for error handling and splitting jobs over multiple machines), and the multiple command approach may lead to overly long command line strings. Peter
sorry for the late reply, i've been away for almost a month. thanks for your work on this, i'll update the tools and upload to toolshed asap. On Tue, May 29, 2012 at 3:35 AM, Peter Cock <p.j.a.cock@googlemail.com>wrote:
On Fri, May 25, 2012 at 4:54 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Edward,
It has taken me a while but I'm how trying to use HMMER3, and do so from within Galaxy.
I've realised that the per sequence and per domain tables from hmmscan and hmmsearch (via the --tblout and --domtblout switches) are NOT tab separated, but space separated to give an eye pleasing column based layout.
However, your wrapper tells Galaxy they are "tabular". As a result, Galaxy treats them like tables with one column, which means all the table operations like filtering on a particular column are not possible. Has this not affected your users?
I ran into some similar problems wrapping other tools giving table based output, and used a wrapper script to make them into tab separated tables for use in Galaxy. e.g. SignalP 3 (spaces), EffectiveT3 (semi-colons).
Would you agree that a wrapper script to reformat the HMMER3 tables into tab-separated tables would be the best solution? Would you accept a code contribution to do this?
Regards,
Peter
Hi Edward,
I've written a simple HMMER3 table to tabular script in Python, https://github.com/peterjc/picobio/blob/master/hmmer/hmmer_table2tabular.py
Would you prefer to:
(a) amend the XML to call HMMER, and then call the conversion script twice.
(b) turn this into a single wrapper script which calls HMMER3 and then converts the two tables (using a multiple command line call with shell semi-colon separators).
(c) do something else?
I favour the wrapper script option as more flexible in the long run (e.g. for error handling and splitting jobs over multiple machines), and the multiple command approach may lead to overly long command line strings.
Peter
On Wed, Jun 27, 2012 at 7:54 PM, Edward Kirton <eskirton@lbl.gov> wrote:
sorry for the late reply, i've been away for almost a month. thanks for your work on this, i'll update the tools and upload to toolshed asap.
Hi Edward, As you will have seen I've (finally) got back to looking at the BLAST database stuff for Galaxy. Hopefully that will get merged soon - but right now I suspect most of their attention is at the conference in Chicago. In terms of local interest, next on the wish list is HMMER3 - so I wanted to see where things stand with your wrapper and getting tab-separated tables for use withing Galaxy. Any joy? Thanks, Peter
participants (4)
-
Dave Clements -
Edward Kirton -
Greg Von Kuster -
Peter Cock