BIRCH/Release To Do list

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*add uniqid to the pipeline to get over the limitation in Phylip that you need to have names <= 10 characters in length.
*add uniqid to the pipeline to get over the limitation in Phylip that you need to have names <= 10 characters in length.
**change all Phylip programs to launch Archaeopteryx instead of ATV.
**Update tutorials for Archaeopteryx
**delete ATV from birchdb
**delete ATV from $BIRCH/java

Revision as of 21:23, 19 May 2013

Mystica Arrow set (with deep) 1.png [return to BIRCH Project]



Convert menus to PCD

  1. Convert BIRCH core menus
  2. Need to come up with an automated way to convert menus in BIRCH/local
  3. Need to refactor paths to files for Help buttons in menus
  4. Add empty PCD directories to local-generic/dat
  5. Update documentation to show how to create PCD menus. Make sure to keep the GDE documentation around as a deprecated package

Move GetBIRCH Python scripts to install-scripts

  1. Move Python scripts to install-scripts
  2. Change GetBIRCH to look for them there
  3. Change birchconfig to look for them there
  4. Make sure we don't lose features that were added to the .sh scripts


birchadmin is a birch system administration tool.

Quick and dirty patch/addon mechanism

We need a way to apply patches to an existing BIRCH install. This should be a very simple mechanism to start with, which will also teach us some things about exactly what it is that we want it to do. Initially, it should probably be nothing more than running a script that downloads a file and untars it, so that the files just go where they are supposed to go with permissions already set.

We need a mechanism to record in $BIRCH/local which addons are installed. This way, when a BIRCH update is installed, we can make sure to re-install any addons.

Definition of an add-on

An add-on includes:


An add-on can either be something new that is installed, or a patch that overwrites existing files, or even a script that runs and changes something. For example, a patch might be as simple as a script that changes important permissions, or changes the name of a file, or does a string substitution to correct an error.


get list of available addons/patches
user selects one or more
foreach addon selected
    cd $BIRCH
    download addon
    gunzip addon.tar.gz
    tar xvfp addon.tar
    cd xxxx.addon.d
    mv contents.tar $BIRCH
    cd $BIRCH
    tar xvfp contents.tar
    cd xxxxx.addon.d
    cat addon_spec.csv >> $BIRCH/local/admin/addons.csv


Fasta3.6 has extensive improvements from 3.5, and we need to reflect that in our online documentation and in biolegato menus.

Command line options

There are many new output options, such as output to key/value pairs, that we should be able to take advantage of.


Each program can generate a man page eg. fasta36 -help. These should be saved as files and made available through the bioLegato Help button.

pairwise alignment programs - output to biolegato

Replace fastaout.csh with a script that will open the output of a pairwise alignment program in blnalign or blpalign.


Upgrade to latest version


Upgrade to latest version

blastcl3 - replace with BLAST+

blastcl3 is now deprecated, in favor of the BLAST+ tools. Apparently, all BLAST+ tools have a -remote commandline switch that sends the search to NCBI, instead of running it locally. blastcl3 requires a socket that remains connected to NCBI for the duration of the search, whereas BLAST+ does not.

Please see

New BLAST+ PCD Menus

BLAST+ 2.2.27

Version 2.2.27 has just been released, too late to get into the current BIRCH release. However, we should upgrade to 2.2.27 in the next release. There are a few bug fixes, as well as some changes in command line options, that should be supported in BioLegato.



Note:we need a program that works with both DNA and proteins


blnalign, blpalign

Break out multiple alignment tasks from bldna and blprotein into new BioLegato instances, blnalign and blpalign, respectively. This improves the object-oriented nature of the various BioLegatos. In particular, it makes it harder to do, for example, phylogeny tasks on sets of unaligned sequences, or to feed sequences with gaps into sequence programs that expect no gaps.

  1. blnalign - extract menus for viewing alignments, phylogeny, removal of gaps
  2. blpalign - extract menus for viewing alignments, phylogeny, removal of gaps
  3. bldna - remove menus for viewing alignments, phylogeny, removal of gaps; alignment progs. call blnalign
  4. blprotein - remove menus for viewing alignments, phylogeny, removal of gaps; alignment progs. call blpalign
  5. birch - add launchers for blpalign, blnalign
  6. revise install scripts to add blpalign and blnalign sections to local.
  7. birchdb - add entries for blnalign and blpalign; change entries for other programs to reflect whether they are run in blnalign or blpalign.
  8. mrtrans - remove from bldna, blprotein and blnalign. Revise menu in blpalign so that it exports the protein alignment, and the only parameter set is the name of the unaligned DNA file.
  9. Revise tutorials
  10. Edit menus - change CopyOut and PasteIn to use .blnalign_clipboard and .blpalign_clipboard; modify Sort and Extract menus to use blnalign and blpalign.
  11. File-->New Window
  12. Update the BioLegato Edit help page to list .blnalign_clipboard and .blpalign_clipboard. While we're there, also mention that Sort is, in fact implemented.



BioLegato for continuous data. This would be an implementation of bltable, targeted at data expressed in real numbers, such as phenotypic data. We would start out with the appropriate programs from Phylip:



1. in bldna, read in GMCAB2, GMCAB3, PEACAB15 and WHTCAB from $birch/tutorials/bioLegato/dotmatrix directory.
2. In name pane, SelectAll; Database --> Features - extract by FeatureKeys. This should give a new bldna window with the coding sequences.
3. Select GMCAB2, GMCAB3, PEACAB15. Group.
4. repeat 2. New bldna window pops up, but it is empty.
5. It is now impossible to Ungroup these sequences.

The problem seems to be how bioLegato exports the sequences, or rather fails to. BL creates a temporary file called temp.xxxx.fea, which is empty. It should contain fasta-formatted sequences. The empty file results in a splitdb job getting into an infinite loop.
There seems to be a separate problem. In step 1, if you never click inside the sequence pane, nothing gets selected. It's not enough to select names. At least once, you must click inside the sequence pane.

String COMMAND = new String( "/bin/csh ../script/browser.failsafe.csh " + BP.homedir + "/public_html/index.html &");
OKAY = runner.runCommand(COMMAND);

In bioLegato, you should probably call all itemmethod's using /bin/sh.

Readseq version 2.1.27 (19-Apr-2008)

    • birch - the high-level launcher for all biolegato and other GUI programs
    • bldata - the successor to dGDE. we will need to come up with a replacement for the old SeqHound web services
    • biolegato - typing 'biolegato' should prompt the user to use either bldna or blprotein

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