BIRCHv3.00
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Contents |
Generate Download Statistics
First attempt using awstats.pl
There wasn't enough support from IST on this, so I decided to write a simple backend and put it on a Bit server. See BIRCH Download Stats
Getbirch Wizard
-
In the Advanced panel, the checkbox for sending stats to BIRCH cannot be unchecked. Why? -
In the Advanced panel, the label and checkbox for sending stats to BIRCH is partly obscured by the bottom edge of the panel. I have only seen this so far on albacore.
Convert BIRCH core menusNeed to refactor paths to files for Help buttons in menusAdd empty PCD directories to local-generic/datUpdate documentation to show how to create PCD menus. Make sure to keep the GDE documentation around as a deprecated package
Installation and Uninstallation
-
make symbolic link from nobirch to nobirch.py and test during install, uninstall, and for individual users. -
test UNINSTALL-birch.py for conditions listed in header comments
Move GetBIRCH Python scripts to install-scripts
- Move Python scripts to install-scripts
- Change GetBIRCH to look for them there
- Change birchconfig to look for them there
- Make sure we don't lose features that were added to the .sh scripts
birchadmin
birchadmin is a birch system administration tool.
launched from birchhas unique graphic canvascan only be run by BIRCH administrator- menus
- File
Switch - use a different copy of BIRCH
- File
- Web
htmldoc.pycustomdoc.pyrun lbirchdb
- InstallAddUpdate
uninstall
- Web
bldna
Two new functions: Import From Text Editor and Export to Text Editor. For example the former would opens up a text editor and accepts a sequence. When the text editor is closed, readseq filters the sequence and inserts it into the current bldna window.The latter would filter the selection into sequin, and make it pop up in an editor. Could this be identical to the existing Import/Export features, but with output to an editor, instead of a file?
Not necessary. Can be handled more intuitively in BioLegato's internal. Copy and Paste functions.SHUFFLE - Switch to xylem_shuffle.py, and generate a random seed, rather than having the user set the seed.
blprotein
Two new functions: Import From Text Editor and Export to Text Editor. For example the former would opens up a text editor and accepts a sequence. When the text editor is closed, readseq filters the sequence and inserts it into the current bldna window.The latter would filter the selection into sequin, and make it pop up in an editor. Could this be identical to the existing Import/Export features, but with output to an editor, instead of a file?Not necessary. Can already be handled by BioLegato's internal Copy and Paste functions.SHUFFLE - Switch to xylem_shuffle.py, and generate a random seed, rather than having the user set the seed.
Output to blnfetch, blpfetch
Currently works for blast, but also needs to work for local fasta.update tutorials
blncbi
MOST CRITICAL: solve the Edirect Perl library dependency problemSolution: Replaced EDirect with BioPython Entrez tools.clean up search of nucleotide and protein databasesget link out working properlyget related working properly- link out to PubMed
update tutorials to include blncbimake sure that blncbi, blnfetch and blpfetch clean up temporary files.- When ncbiquery.py is run from the command line, we don't see leftover temporary files. The file names when run from blncbi all have names like bioxxxxxxx.tmp, and are 0 length files. So the problem is with blncbi.
- The problem appears to be with the out2 variable, which is the file read when BioLegato reads the results into the current window. It is fixed by setting save to false for out2. BioLegato seems to know enough to wait until out2 has been read before deleting it, so we don't have to explicitly delete it.
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 http://1.usa.gov/xbErSV
SEQUIN
Upgrade to latest version
Updated to Version 13.70 on linux-x86_64 and MacOSX. NCBI appears to no longer be supporting Solaris. Consequently, the solaris-sparc and solaris-amd64
binaries have been updated to Version 13.05, the latest version for these platforms.
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.
blnalign - extract menus for viewing alignments, phylogeny, removal of gapsblpalign - extract menus for viewing alignments, phylogeny, removal of gapsbldna - remove menus for viewing alignments, phylogeny, removal of gaps; alignment progs. call blnalignblprotein - remove menus for viewing alignments, phylogeny, removal of gaps; alignment progs. call blpalignbirch - add launchers for blpalign, blnalignrevise install scripts to add blpalign and blnalign sections to local.
programs to display sequence logos
birchdb - add entries for blnalign and blpalign; change entries for other programs to reflect whether they are run in blnalign or blpalign.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.Revise tutorialsEdit menus - change CopyOut and PasteIn to use .blnalign_clipboard and .blpalign_clipboard; modify Sort and Extract menus to use blnalign and blpalign.File-->New WindowUpdate the BioLegato Edit help page to list .blnalign_clipboard and .blpalign_clipboard. While we're there, also mention that Sort is, in fact implemented.weblogo - Apparently, weblogo requires ghostscript to generate all file formats except for eps. Although gs seems to be standard on Linux, it is not on OSX. With the default settings, blpalign/blnalign will not produce an output window. Solution: Make EPS the default format. weblogo.py doesn't require ghostscript for EPS, so this will work on all configurations. The other choices (PDF, PNG, JPEG) will work if ghostscript is installed.
Binaries
linux-x86_64 |
linux-intel |
osx-x86_64 |
solaris-sparc |
solaris-amd64 |
|
BLAST+ |
v2.2.30 |
v2.2.30 |
v2.2.30 |
v2.2.27 requires libzo2.so.2 |
v2.2.27 |
FASTA3 |
36.3.6 |
36.3.7a |
36.3.6 |
36.3.6 Database search programs reverted to fasta35, fastx35, fasty35 tfastx35 tfasty35 because of execution errors |
36.3.6 Database search programs reverted to fasta35, fastx35, fasty35 tfastx35 tfasty35 because of execution errors |
Sequin |
13.70 |
13.05, the latest version for these platforms. |
13.70 |
13.05, the latest version for these platforms. |
13.05, the latest version for these platforms. |
t_coffee |
11.8 |
v8.14 |
v8.14 (later versions either won't compile on albacore or give error messages) |
8.14 later versions not tried |
8.14 later versions not tried |
Phylip |
3.69 |
3.69 |
3.69 |
3.69 |
3.69 |