Turnsek, Jernej | 26 May 02:09 2016
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Re: Cannot download/find BPbl2seq module

<!-- P {margin-top:0;margin-bottom:0;} -->

Wonderful. I'll give it a shot with v1.5.2 or lower then.


Thank you all again!


Jernej


From: Fields, Christopher J <cjfields <at> illinois.edu>
Sent: Wednesday, May 25, 2016 5:10:35 PM
To: Turnsek, Jernej
Cc: Mark Jensen; Brian Osborne; bioperl-l <at> bioperl.org
Subject: Re: [Bioperl-l] Cannot download/find BPbl2seq module
 
Yep, those tools used Ian’s old BPLite, see here:


These would last be in the 1.5.2 release series and were removed prior to v1.6 as their functionality was largely subsumed by Bio::SearchIO.

chris

On May 25, 2016, at 4:06 PM, Turnsek, Jernej <turnsek <at> fas.harvard.edu> wrote:

Thanks everyone for your thoughts and suggestions, especially thanks for the github page with older BioPerl releases. I found this website from winter 07' stating:

"Bioperl's older BLAST report parsers - BPlite, BPpsilite, BPbl2seq and Blast.pm - are no longer supported but since legacy Bioperl scripts have been written which use these objects, they are likely to remain within Bioperl for some time."

The error message I see is here:

<OAF_error.png>

Jernej
From: Fields, Christopher J <cjfields <at> illinois.edu>
Sent: Wednesday, May 25, 2016 4:39:28 PM
To: Mark Jensen
Cc: Turnsek, Jernej; bioperl-l <at> bioperl.org
Subject: Re: [Bioperl-l] Cannot download/find BPbl2seq module
 
One thing to note: the OAF tools were last released in 2008.  There is some possibility that newer versions of bioperl may or may not work with this; if you run into problems I suggest using one of the older releases:


chris

On May 25, 2016, at 2:12 PM, Mark A Jensen <maj <at> fortinbras.us> wrote:

Oops, I am wrong about this. 
There is no such module BPbl2seq in any distribution, there is a module Bio::AlignIO::bl2seq. My guess is this a module created by the author of the oaf tool that uses bioperl under the hood. You can get a missing module error sometimes if the module.is present but contains a syntax error.
On Wed, May 25, 2016 at 2:45 PM, Mark A Jensen <maj <at> fortinbras.us> wrote:

Jernej, this is a script that should appear in your path if you install bioperl from cpan and choose yes for the question "install scripts?"
Mark
On Wed, May 25, 2016 at 1:21 PM, Turnsek, Jernej <turnsek <at> fas.harvard.edu> wrote:


Dear BioPerl community,


I am trying to use OAF - a Perl-based tool to analyze cDNA data - with a goal to detect antizyme or antizyme-like sequences. The publication describing the tool is available here. I installed Perl (v5.22.2) and BioPerl (v1.6.924) which I believe came with HMMER. I haven't installed FASTA and BLAST locally yet - they are both optional (see this link). What I tried to do next is replicate the "my_sequence" example listed on this website using the attached .pl script and .fasta file, but ended up stuck with the error stating I am missing a necessary BioPerl module -BPbl2seq - which I couldn't download from CPAN. I tried to locate it manually online, but it looks like it doesn't exist anymore. I've talked to some Perl specialists around here and it seems like I should reinstall Perl and BioPerl versions that were present around the time this software was developed (2007/2008) with a rationale that they will carry all the necessary modules including BPbl2seq

I'd greatly appreciate if you could provide me with some tips on how to proceed. I am working on a Lenovo Yoga PC, 64-bit Windows 8.1.



I look forward to hearing from you.

Thank you and kind regards,

Jernej Turnsek






Jernej Turnsek 
Ph.D. Candidate | Pamela Silver's Lab 
Department of Systems Biology | Harvard Medical School
200 Longwood Ave | Boston, MA 02115
(617) 797-5386 | Web | LinkedIn |  <at> SynEnthu
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Matthew | 25 May 22:08 2016
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barcode split a paired-end fastq file

Are there any BioPerl modules that would help to split a barcoded fastq 
file ?

I have tried FASTX-toolkit, but it does not work on paired-end data.

The file I have been given is paired-end but a single file, and I have a 
list of 8 or so 4 letter barcodes.

Matthew
Turnsek, Jernej | 25 May 18:44 2016
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Cannot download/find BPbl2seq module

Dear BioPerl community,


I am trying to use OAF - a Perl-based tool to analyze cDNA data - with a goal to detect antizyme or antizyme-like sequences. The publication describing the tool is available here. I installed Perl (v5.22.2) and BioPerl (v1.6.924) which I believe came with HMMER. I haven't installed FASTA and BLAST locally yet - they are both optional (see this link). What I tried to do next is replicate the "my_sequence" example listed on this website using the attached .pl script and .fasta file, but ended up stuck with the error stating I am missing a necessary BioPerl module - BPbl2seq - which I couldn't download from CPAN. I tried to locate it manually online, but it looks like it doesn't exist anymore. I've talked to some Perl specialists around here and it seems like I should reinstall Perl and BioPerl versions that were present around the time this software was developed (2007/2008) with a rationale that they will carry all the necessary modules including BPbl2seq


I'd greatly appreciate if you could provide me with some tips on how to proceed. I am working on a Lenovo Yoga PC, 64-bit Windows 8.1.


I look forward to hearing from you.

Thank you and kind regards,

Jernej Turnsek




Jernej Turnsek 
Ph.D. Candidate | Pamela Silver's Lab 
Department of Systems Biology | Harvard Medical School
200 Longwood Ave | Boston, MA 02115
(617) 797-5386 | Web | LinkedIn | <at> SynEnthu
Attachment (oaf.pl): application/octet-stream, 12 KiB
Attachment (mysequence.fasta): application/octet-stream, 1289 bytes
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James E Keenan | 16 May 01:41 2016
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Need CPAN release to clear up CPANtesters test failure reports

The other day I was looking for unanswered Perl-tagged questions on 
stackoverflow.  I came across this one:

http://stackoverflow.com/questions/36985090/extracting-and-joining-exons-from-multiple-sequence-alignments

To answer it I tried to install BioPerl from CPAN but got multiple test 
failures.  I then checked out the BioPerl page on CPANtesters and saw 
that your latest CPAN distribution has experienced massive test failures 
on many versions of Perl and several different operating systems.  See: 
  http://matrix.cpantesters.org/?dist=BioPerl+1.6.924

I subsequently located your github site at 
https://github.com/bioperl/bioperl-live, from which I was able to fork. 
  When I attempted to build locally, I was pleasantly surprised to find 
all tests run by ./Build test were PASSing.  The only problem I saw was 
a "missing or corrupt MANIFEST" message, for which I have supplied this 
pull request:  https://github.com/bioperl/bioperl-live/pull/150.

Your last CPAN release was in July 2014.  I strongly advise that you do 
a CPAN release of BioPerl ASAP so that your project does not suffer 
reputational damage from all those test failure reports.  At the same 
time, I urge you to go through the bug reports at 
https://rt.cpan.org/Public/Dist/Display.html?Name=BioPerl.  It's likely 
that HEAD on github resolves some of these.

Thank you very much.
Jim Keenan
Fields, Christopher J | 8 Apr 23:39 2016
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Bioperl Wiki update

Just a note: the Bioperl wiki page at bioperl.org went down a few days ago due to a server hack that we’re
investigating.  Luckily, Brian Osborne had been working on migrating key documentation such as
installation and HOWTO documents to Github Pages, hosted here:

https://github.com/bioperl/bioperl.github.io

Due to the wiki downtime we decided to go ahead and switch the DNS over to the new site.  So, major thanks to
Brian for initiating the move, as well as Paul Cantalupo and Francisco Ossandon for helping with document migration!

Depending on the severity of the issue we may have a link to a static mediawiki instance set up in the future;
in the meantime, please let us know if there are any particular bioperl-related documents that you would
like to see moved over.

Thanks,

chris

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Fields, Christopher J | 2 Mar 18:59 2016
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Test email

Plz ignore, kthxbye
Scott Cain | 26 Feb 18:50 2016
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GMOD 2016 meeting

Hello all,

I am pleased to announce that details have been finalized for the 2016 GMOD meeting.  It will take place immediately following the Galaxy Community Conference at Indiana University in Bloomington, IN on June 30 and July 1.  We're still working on agenda details, so if you have suggestions or would like to present, please let me know.

For registration information, please see:


And for other information about the meeting, keep an eye on:


I look forward to seeing you there!
Scott


--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research
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Fields, Christopher J | 9 Feb 19:03 2016
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FW: [Open-bio-l] Let's get started with Google Summer of Code 2016

Kai Blin has graciously accepted heading up this year’s GSoC (with some help from Raoul Bonnal); see
below for the original announcement.  Several ideas are present for BioPerl, including submission of
project ideas for Perl 6.  This could run the gamut from writing up new code for BioPerl to creating useful
library bindings for Perl 6.  

Also, we will need potential mentors for projects to help out.  This could be for Perl-related projects but
also for other projects where you may have expertise.  Discussions will be happening on the OBF/GSoC list
should anyone want to suggest project ideas or help mentor.

http://lists.open-bio.org/mailman/listinfo/gsoc

Thanks,

chris

On 2/9/16, 9:43 AM, "Open-Bio-l on behalf of Kai Blin"
<open-bio-l-bounces+cjfields=illinois.edu <at> mailman.open-bio.org on behalf of
kblin <at> biosustain.dtu.dk> wrote:

>Dear Open Bioinformatics community,
>
>Google is now accepting applications for mentoring organizations for the 2016 installment of the Google
Summer of Code. You can find out a bit about the Google Summer of Code from an OBF perspective on our wiki at
http://www.open-bio.org/wiki/Google_Summer_of_Code. My apologies for the 2015 material still on
there, but I've been fighting with the OpenID account creation on our wiki, and have not won so far. Still,
most of the material still applies for this year.
>
>In order to actually collect a number of interesting project ideas that we could have students work on, we
need your help as a community. Please join us on the OBF/GSoC mailing list
(http://lists.open-bio.org/mailman/listinfo/gsoc) so we can get rolling.
>
>I would love to get a good list of proposals together until Wednesday, February 17th. To get a feeling what
some nice project ideas would look like, have a look at our ideas list for 2015
(http://www.open-bio.org/wiki/Google_Summer_of_Code_2015_Ideas). As in the last years, project
ideas from all the OBF member projects are welcome. Additionally, we would like to invite other
bioinformatics projects that are connected to the OBF to join us in our GSoC application. Connected
projects would include projects that are heavy users of the Bio* libraries or similar. It would be ideal if
all project ideas could be backed by two mentors.
>
>Feel free to forward this message to your respective OBF member projects, or connected bioinformatics community.
>
>Kind regards from the OBF GSoC team,
>
>Kai Blin,
>OBF administrator for GSoC 2016
>
>--
>Kai Blin                                           kblin <at> biosustain.dtu.dk  
>PostDoc / Scientific Software Engineer
>DTU Biosustain                                     http://www.biosustain.dtu.dk/
>Building Thujahuset, room 2.L.09
>DK - 2970 Hørsholm
>Denmark
>mobile: +45 93511306                               twitter:  <at> kaiblin
>
>
>
>
>_______________________________________________
>Open-Bio-l mailing list
>Open-Bio-l <at> mailman.open-bio.org
>http://mailman.open-bio.org/mailman/listinfo/open-bio-l

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Hilmar Lapp | 26 Jan 21:01 2016
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Re: Call for Org Admins for OBF's 2016 Google Summer of Code participation

Dear all,

I’m very pleased to announce that Kai Blin will be OBF’s org admin for our 2016 GSoC program
participation. Please join me in offering Kai our full support. You can reach Kai at
kblin <at> biosustain.dtu.dk, and if you haven’t already you’ll hear from him soon. Raoul Bonnal, who
was leading our GSoC participation in the last two years, will work with Kai as the backup org admin.

On behalf of the Board and the community at large, my thanks and kudos to both Kai and Raoul for stepping up.

 -hilmar

> On Jan 15, 2016, at 5:42 PM, Hilmar Lapp <hlapp <at> drycafe.net> wrote:
> 
> The 2016 Google Summer of Code (GSoC) is coming up soon. The published timeline [1] puts the mentoring
organization applications from Feb 8 to 19.
> 
> OBF participated on behalf of our member projects from 2010-2012, and in 2014. Those participations were
both important and successful. Through them, our projects gained new contributors, new features, and
new community members. The mentors involved from our projects learned as much from the experience as the
students, and formed bonds. Starting in 2012 and in particular in 2014, we also committed to “paying it
forward” on the organization level, welcoming a much broadened scope of projects to participate under
our umbrella (see [2] for a summary). Finally, the mentoring organization payments have allowed OBF to
sponsor community events, student travel awards, and infrastructure.
> 
> To participate this year, we have to appoint 2-3 people as primary and backup organization
administrators. This is an important role, and we are looking for people from our community to step
forward to serve. Our org admins from previous years (Eric Talevich and Raoul Bonnal) remain available
for backup and guidance, but are unfortunately not in a position to take the lead org admin role. 
> 
> ## What does an org admin do?
> 
> An org admin’s role is in many ways that of a cat herder with a vision. The whole team of mentors and admins
is what creates the experience for the students, but it falls on the org admin to “keep it together.”
Google holds the mentoring organization, not its mentors, accountable for the actions (or non-actions)
of its mentors or community, and it falls on the org admin to carry that accountability through to the
org’s mentors. The org admin’s responsibilities include:
> 
> 	• Shaping and setting the overall vision (including scope) for our program participation.
> 	• Serving as the primary contact for our participation to Google, to mentors, and to students.
> 	• Shepherding our mentoring organization application, and submitting it.
> 	• Determining processes and rules for mentors as well as students that promote transparency,
fairness, and protect from late-in-the-game surprises.
> 	• Knowing GSoC rules and processes, and making sure ours are consistent with them.
> 	• Reminding participants of rules, and enforcing them in the event it is necessary.
> 	• Mediating, and sometimes arbitrating between students and mentors when needed.
> 	• Ensuring that GSoC timelines are met by everyone.
> 
> OBF’s 2016 program participation may continue or even extend from previous years the broadening of
scope for participating projects. We could also partner with other open-source bioinformatics project
communities to form a joint umbrella. These questions are part of setting the vision for our program
participation, and intentionally not pre-set. Although the OBF Board retains a veto right, we have
always given our community leaders full trust and full latitude once appointed.
> 
> The person we are looking for will genuinely care about the well-being of our communities; cares about
students and student learning; is well organized; stays calm in email storms; communicates clearly; has
good people skills; and generally is known as a good listener.
> 
> ## How to respond?
> 
> If you are interested in helping us out in this role, please email us by Thursday Jan 21, 2016, a statement at
board <at> open-bio.org explaining how you would fit well in this role, and what your vision for our GSoC
participation is. You need not be a developer or programmer to respond, but having been active in some
capacity in at least one of our project’s communities will certainly be very valuable. Please include
in your email a brief summary of such activities, or a pointer to where they can be looked up online.
> 
> We are looking forward to hearing from you!
> 
> Hilmar Lapp, OBF President, on behalf of the OBF Board of Directors
> 
> [1] https://developers.google.com/open-source/gsoc/timeline?hl=en
> [2] http://news.open-bio.org/news/2015/02/obf-gsoc-2014-wrapup/
> 
> -- 
> Hilmar Lapp -:- lappland.io
> 

--

-- 
Hilmar Lapp -:- lappland.io

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Carnë Draug | 20 Jan 21:45 2016
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distzilla pluginbundle: bioperl vs BioPerl

Hi

I was searching for the bioperl distzilla plugin bundle when I found
out that there are currently two distributions with the difference
on the capitalization of bioperl:

    https://metacpan.org/pod/Dist::Zilla::PluginBundle::Bioperl
    https://metacpan.org/pod/Dist::Zilla::PluginBundle::BioPerl

The first one (out of date) is the first autocomplete suggestion on
metacpan when searching for bioperl.  I got confused for a while,
assumed that we had regraded to the previous pluginbundle for some
weird reason and went to look into the actual repository.

It should probably be removed.  Is that possible?

Carnë

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Hilmar Lapp | 15 Jan 23:47 2016
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Call for Org Admins for OBF's 2016 Google Summer of Code participation

(apologies to those receiving duplicates - we are trying to reach our community at large)

The 2016 Google Summer of Code (GSoC) is coming up soon. The published timeline [1] puts the mentoring
organization applications from Feb 8 to 19.

OBF participated on behalf of our member projects from 2010-2012, and in 2014. Those participations were
both important and successful. Through them, our projects gained new contributors, new features, and
new community members. The mentors involved from our projects learned as much from the experience as the
students, and formed bonds. Starting in 2012 and in particular in 2014, we also committed to “paying it
forward” on the organization level, welcoming a much broadened scope of projects to participate under
our umbrella (see [2] for a summary). Finally, the mentoring organization payments have allowed OBF to
sponsor community events, student travel awards, and infrastructure.

To participate this year, we have to appoint 2-3 people as primary and backup organization
administrators. This is an important role, and we are looking for people from our community to step
forward to serve. Our org admins from previous years (Eric Talevich and Raoul Bonnal) remain available
for backup and guidance, but are unfortunately not in a position to take the lead org admin role. 

## What does an org admin do?

An org admin’s role is in many ways that of a cat herder with a vision. The whole team of mentors and admins is
what creates the experience for the students, but it falls on the org admin to “keep it together.”
Google holds the mentoring organization, not its mentors, accountable for the actions (or non-actions)
of its mentors or community, and it falls on the org admin to carry that accountability through to the
org’s mentors. The org admin’s responsibilities include:

	• Shaping and setting the overall vision (including scope) for our program participation.
	• Serving as the primary contact for our participation to Google, to mentors, and to students.
	• Shepherding our mentoring organization application, and submitting it.
	• Determining processes and rules for mentors as well as students that promote transparency,
fairness, and protect from late-in-the-game surprises.
	• Knowing GSoC rules and processes, and making sure ours are consistent with them.
	• Reminding participants of rules, and enforcing them in the event it is necessary.
	• Mediating, and sometimes arbitrating between students and mentors when needed.
	• Ensuring that GSoC timelines are met by everyone.

OBF’s 2016 program participation may continue or even extend from previous years the broadening of
scope for participating projects. We could also partner with other open-source bioinformatics project
communities to form a joint umbrella. These questions are part of setting the vision for our program
participation, and intentionally not pre-set. Although the OBF Board retains a veto right, we have
always given our community leaders full trust and full latitude once appointed.

The person we are looking for will genuinely care about the well-being of our communities; cares about
students and student learning; is well organized; stays calm in email storms; communicates clearly; has
good people skills; and generally is known as a good listener.

## How to respond?

If you are interested in helping us out in this role, please email us by Thursday Jan 21, 2016, a statement at
board <at> open-bio.org explaining how you would fit well in this role, and what your vision for our GSoC
participation is. You need not be a developer or programmer to respond, but having been active in some
capacity in at least one of our project’s communities will certainly be very valuable. Please include
in your email a brief summary of such activities, or a pointer to where they can be looked up online.

We are looking forward to hearing from you!

Hilmar Lapp, OBF President, on behalf of the OBF Board of Directors

[1] https://developers.google.com/open-source/gsoc/timeline?hl=en
[2] http://news.open-bio.org/news/2015/02/obf-gsoc-2014-wrapup/

--

-- 
Hilmar Lapp -:- lappland.io

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Gmane