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The BioPerl Web site: http://bioperl.org
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Updates to HOWTOs #1

Closed cjfields closed 8 years ago

cjfields commented 8 years ago

Sign up here for HOWTO doc updates. So far:

@bosborne : Beginners, SearchIO, SeqIO,Restriction_Enzyme_Analysis @pcantalupo : BlastPlus, Writing_BioPerl_Tests, Getting_Genomic_Sequences, PAML, PhyloXML, PopGen, Simple_web_analysis, SubmitPatch, Nexml, Glyphs @majensen : Tiling, EUtilities WebServices, Short-read_assemblies_with_BWA, Short-read_assemblies_with_maq, Trees @cjfields : EUtilities Cookbook, Feature-Annotation, AlignIO_and_SimpleAlign, Bioperl_Objects, Nexml

Remaining: Graphics Local_Databases OBDA OBDA_Flat_databases PhylogeneticAnalysisPipeline Trees

majensen commented 8 years ago

Updated list in comment-

pcantalupo commented 8 years ago

anybody having problems rendering an ftp link in Markdown? I cannot get

[blast+](ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)

to show as a hyperlink.

see: blast+

majensen commented 8 years ago

hmm - is it the '+'?

pcantalupo commented 8 years ago

doesn't work without the plus

majensen commented 8 years ago

blast+ blast+

Ah, see above, MD doesn't get "ftp" as a protocol maybe

hyphaltip commented 8 years ago

however http link also works so you dont need the ftp protocol link.

pcantalupo commented 8 years ago

thank you

pcantalupo commented 8 years ago

Some of the HOWTOs have irritating non-breaking spaces in the code which does not look good when converted to html. I used the following command to convert them to regular spaces in BlastPlus.md:

perl -pe 's/\xc2\xa0/ /g' BlastPlus.md

Hopefully this will help somebody else.

bosborne commented 8 years ago

Thanks Paul, ran that over all the files.

On Dec 1, 2015, at 12:33 AM, Paul Cantalupo notifications@github.com wrote:

Some of the HOWTOs have irritating non-breaking spaces in the code which does not look good when converted to html. I used the following command to convert them to regular spaces in BlastPlus.md:

perl -pe 's/\xc2\xa0/ /g' BlastPlus.md Hopefully this will help somebody else.

— Reply to this email directly or view it on GitHub https://github.com/bioperl/bioperl.github.io/issues/1#issuecomment-160858319.

pcantalupo commented 8 years ago

Is there a facility in Markdown for creating a Table of Contents like that in the HOWTO Wiki?

bosborne commented 8 years ago

It currently does not work:

http://ajoz.github.io/2014/06/29/i-want-my-github-flavored-markdown/

I went through the same process as this poster, trying different MD interpreters in search of one that could do code blocks. Unfortunately the one that does does not do TOC’s.

On Dec 1, 2015, at 9:30 AM, Paul Cantalupo notifications@github.com wrote:

Is there a facility in Markdown for creating a Table of Contents like that in the HOWTO Wiki?

— Reply to this email directly or view it on GitHub https://github.com/bioperl/bioperl.github.io/issues/1#issuecomment-160984114.

bosborne commented 8 years ago

Chris, I fixed the Feature-Annotation HOWTO.

On Dec 1, 2015, at 9:30 AM, Paul Cantalupo notifications@github.com wrote:

Is there a facility in Markdown for creating a Table of Contents like that in the HOWTO Wiki?

— Reply to this email directly or view it on GitHub https://github.com/bioperl/bioperl.github.io/issues/1#issuecomment-160984114.

bosborne commented 8 years ago

Keeping track, these HOWTOs look done: Beginners, Feature-Annotation, BlastPlus, Utilities_Cookbook, SearchIO, SeqIO, Getting Genomic Sequences, AlignIO and SimpleAlign, and Writing BioPerl Tests.

Remaining:

EUtilities_Web_Service Glyphs Graphics Nexml OBDA OBDA_Flat_databases PAML PhyloXML PhylogeneticAnalysisPipeline PopGen Restriction_Enzyme_Analysis Short-read_assemblies_with_BWA Short-read_assemblies_with_maq Simple_web_analysis SubmitPatch Tiling Trees Local_Databases Bioperl_Objects

Some of these are incomplete, never finished. Comment them out from the list online?

bosborne commented 8 years ago

Remaining:

EUtilities_Web_Service Glyphs Graphics Nexml OBDA PAML PhyloXML PhylogeneticAnalysisPipeline PopGen Restriction_Enzyme_Analysis Short-read_assemblies_with_BWA Short-read_assemblies_with_maq Simple_web_analysis SubmitPatch Tiling Trees Local_Databases Bioperl_Objects

majensen commented 8 years ago

Tiling is merged in.

bosborne commented 8 years ago

Remaining:

EUtilities Web Service HOWTO Glyphs HOWTO Graphics HOWTO Nexml HOWTO PAML HOWTO PhyloXML HOWTO PopGen HOWTO Restriction Enzyme Analysis HOWTO Short-read assemblies with BWA HOWTO Short-read assemblies with maq HOWTO Simple web analysis HOWTO SubmitPatch HOWTO Trees HOWTO Bioperl Objects HOWTO

pcantalupo commented 8 years ago

I'll take the P's: PAML, PhyloXML, PopGen

majensen commented 8 years ago

BWA is merged in.

cjfields commented 8 years ago

I'll work on Restriction Enzyme Analysis and Trees/PhyloXML/NeXML in addition to the Bioperl Objects I already have. Also, thanks for the work on Feature-Annotation @bosborne ! I kinda fell off the grid for a few days taking care of a sick five-year old (who is doing a lot better now)

bosborne commented 8 years ago

Chris,

Restriction Enzyme Analysis is done. Yes, it’s all being taken away from you.

;-)

Here is what remains:

EUtilities Web Service HOWTO Glyphs HOWTO Graphics HOWTO Nexml HOWTO PAML HOWTO PhyloXML HOWTO PopGen HOWTO Short-read assemblies with maq HOWTO Simple web analysis HOWTO SubmitPatch HOWTO Trees HOWTO Bioperl Objects HOWTO

BIO

On Dec 4, 2015, at 5:30 PM, Chris Fields notifications@github.com wrote:

I'll work on Restriction Enzyme Analysis and Trees/PhyloXML/NeXML in addition to the Bioperl Objects I already have. Also, thanks for the work on Feature-Annotation @bosborne https://github.com/bosborne ! I kinda fell off the grid for a few days taking care of a sick five-year old (who is doing a lot better now)

— Reply to this email directly or view it on GitHub https://github.com/bioperl/bioperl.github.io/issues/1#issuecomment-162100095.

cjfields commented 8 years ago

@bosborne that's completely fine by me :smile:

I noticed some oddities with the Bioperl Objects one (some things have gone missing in the conversion).

pcantalupo commented 8 years ago

@cjfields I started working on PhyloXML and will be done soon. Do you want me to finish it up and commit it?

cjfields commented 8 years ago

Go ahead, that works for me.

On Dec 5, 2015, at 7:27 AM, Paul Cantalupo notifications@github.com<mailto:notifications@github.com> wrote:

@cjfieldshttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cjfields&d=BQMCaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=XrufMM2gcyCefwAHUIGFjhXRSMnq4jb7J_5_5rNe1HU&s=7VG0esve3tiVsbuDa3IenpZvEHFDBwmr7abwVmCoWEo&e= I started working on PhyloXML and will be done soon. Do you want me to finish it up and commit it?

— Reply to this email directly or view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bioperl_bioperl.github.io_issues_1-23issuecomment-2D162184536&d=BQMCaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=XrufMM2gcyCefwAHUIGFjhXRSMnq4jb7J_5_5rNe1HU&s=FML6H5Hkj1BQyxJQ-Ijl-J4gragitUeDHj6ddUZvBQI&e=.

majensen commented 8 years ago

Maq is merged in.

majensen commented 8 years ago

I'll do EUtil Web Svc and Trees

cjfields commented 8 years ago

@majensen I was planning on taking Trees but haven't started yet. If you've started then it's all yours, just let me know.

majensen commented 8 years ago

Too late @cjfields , Trees merged in!

cjfields commented 8 years ago

All, looks like templates like {{CPAN|Bio::Seq}} are silently dropped; lots of these in the 'Bioperl Objects' HOWTO:

MW (from the 'Brief descriptions' section')

===Brief descriptions===

This section describes various Bioperl sequence objects. Many people using Bioperl will never know, or need to know, what kind of sequence object they are using. This is because the {{CPAN|SeqIO}} module creates exactly the right type of object when given a file or a filehandle or a string.

{{CPAN|Bio::Seq}} is the central sequence object in bioperl. When in doubt this is probably the object that you want to use to describe a DNA, RNA or protein sequence in bioperl. Most common sequence manipulations can be performed with Seq.

Converted Markdown

### Brief descriptions

This section describes various Bioperl sequence objects. Many people using Bioperl will never know, or need to know, what kind of sequence object they are using. This is because the module creates exactly the right type of object when given a file or a filehandle or a string.

is the central sequence object in bioperl. When in doubt this is probably the object that you want to use to describe a DNA, RNA or protein sequence in bioperl. Most common sequence manipulations can be performed with Seq.

I can reconvert from the original mediawiki but it may be worth checking how prevalent these are (they mainly seemed relegated to the end).

majensen commented 8 years ago

They're all over the place. I have just been reading down the original howtos and adding the links in. I have a little emacs skeleton for it:

(define-skeleton bioperl-module-md-link
  "Insert a BioPerl module with link to MetaCPAN pod"
  "Module: "
  "[Bio::" str "](https://metacpan.org/pod/Bio::" str ")")

(global-set-key (kbd "C-c C-l") 'bioperl-module-md-link)

You do ctrl-c ctrl-l and then enter "SearchIO" or whatever at the 'Module:' prompt.

majensen commented 8 years ago

EUtilities Web Services merged in.

pcantalupo commented 8 years ago

@bosborne Hi, can you give us an update on what is done and what is left to do?

bosborne commented 8 years ago

Paul,

Looks like these are not done:

  • Glyphs HOWTO
  • Graphics HOWTO
  • Nexml HOWTO
  • SubmitPatch HOWTO

    • These are:

  • PopGen HOWTO
  • Beginners HOWTO
  • Feature-Annotation HOWTO
  • BlastPlus HOWTO
  • EUtilities Cookbook HOWTO
  • SearchIO HOWTO
  • SeqIO HOWTO
  • Getting Genomic Sequences HOWTO
  • AlignIO and SimpleAlign HOWTO
  • Writing BioPerl Tests HOWTO
  • OBDA Flat Databases HOWTO
  • Tiling HOWTO
  • Local Databases
  • OBDA HOWTO
  • Restriction Enzyme Analysis HOWTO
  • Short-read assemblies with BWA HOWTO
  • Short-read assemblies with maq HOWTO
  • Trees HOWTO
  • EUtilities Web Service HOWTO
  • PAML HOWTO
  • PhyloXML HOWTO
  • Bioperl Objects HOWTO
  • Simple Web Analysis HOWTO
  • Advanced BioPerl HOWTO

    • Brian O.

    On Dec 8, 2015, at 1:30 PM, Paul Cantalupo notifications@github.com wrote:

    @bosborne https://github.com/bosborne Hi, can you give us an update on what is done and what is left to do?

    — Reply to this email directly or view it on GitHub https://github.com/bioperl/bioperl.github.io/issues/1#issuecomment-162971269.

    pcantalupo commented 8 years ago

    ok, got SubmitPatch and Nexml done...I'll tackle Glyphs and Graphics next.

    pcantalupo commented 8 years ago

    @bosborne are you going to finish up Graphics HOWTO or should I take care of the rest?

    bosborne commented 8 years ago

    @pcantalupo I did a few edits on Graphics this AM, I believe it is done. And with that, we are finished this task!

    majensen commented 8 years ago

    \o/

    On Thu, Dec 10, 2015 at 8:41 AM, Brian Osborne < notifications@github.com [notifications@github.com] > wrote: Closed #1 [https://github.com/bioperl/bioperl.github.io/issues/1] .

    — Reply to this email directly or view it on GitHub [https://github.com/bioperl/bioperl.github.io/issues/1#event-488180774] .[https://github.com/notifications/beacon/AAFAmRbBDhWpLj6vl2dKKhZjl53B8LiQks5pOXkUgaJpZM4GrmBP.gif]