Nomenclature of commands for biolegato
From Bioinformatics.Org Wiki
- We'll start a new nomenclature of commands for biolegato:
- birch - the high-level launcher for all biolegato and other GUI programs. The menu structure should be something like this:
- DNA
- bldna
- Sequin
- MWCalculator
- Protein
- blprotein
- Cn3D
- Cn3D script not found within /home/psgendb/script
- Cn3D platform dependent; is not available for solaris amd64, added platform specifications 'SLlM'
- Cn3D script not found within /home/psgendb/script
- Multiple sequence alignment
- bldna
- blprotein
- Jalview
- Markers
- blmarker
- Genographer
- Minor error when opening program "$BIRCH/java/genographer/doc/operation.html (Permission denied)"
- Although when I go to this directory and try to open operation.html, it works...
- Minor error when opening program "$BIRCH/java/genographer/doc/operation.html (Permission denied)"
- Phylogeny
- bltree
- Mesquite
- DNA
- birch - the high-level launcher for all biolegato and other GUI programs. The menu structure should be something like this:
NoClassDefFoundError while loading: mesquite.distance.SharedProportionalDistance.SharedProportionalDistance Note: (Mesquite): Error while loading mesquite.distance.SharedProportionalDistance.SharedProportionalDistance. It appears that a component of Mesquite or a required library is missing.
Details: java.lang.NoClassDefFoundError: mesquite/distance/SharedProportionalDistance/SharedProportionalDistance$SharedProportionTD
diverse dmanager mb meristic molec ornamental pairwise rhetenor search tol treefarm iText jama jsci pal trunk
Note: (Mesquite): File cannot be written. It may be locked or open in another application. (4; Path: /home/u13/umchan94/public_html/birch/java/Mesquite_Folder/settings/minimal/Installer/receipts.xml)
- Made SharedProportionalDistance$SharedProportionTD class; got more errors but they are minor ones
- ATV
- Treetool
- Minor error when closing program: "Xview warning: notifier error: unknown client"
- Data mining
- Seahawk
- seahawk: test: argument expected
- java version 1.6 or later ---> we must parse to check which version of java the user has
- Seahawk
- Sequencing and assembly
- Traceview
- Too few arguments- Usage: TraceView gzip'ped_trace_filename
- REMOVED
- Traceview
- Genome annotation
- Bluejay
- Artemis
- Transcriptomics
- ArrayNorm
- Tmev
- Midas
- Usage: /usr/local/bin/midas {auth|latest|summary|recent} [options]
- What kind of data, if any, is allowed to be read into birch?
- (best choice for right now) If birch is nothing more than a file launcher, no data should be read into birch
- Take away 'File' and "Edit' menus. It is part of GDE_MAKEMENUS_DIR
- Another approach is that ANY kind of data can be read into birch, and is used as input for launching programs from birch
- A third possibility is that the birch canvas contains filenames, that could be used as input for launchers
- (best choice for right now) If birch is nothing more than a file launcher, no data should be read into birch
- What kind of data, if any, is allowed to be read into birch?
- bldna - the successor to GDE. 'biolegato' will be a symbolic link to bldna, for backward compatability.
- blprotein - biolegato for proteins. blprotein will contain all the protein methods from biolegato, which will be removed from biolegato to create bldna.
- bldata - the successor to dGDE. we will need to come up with a replacement for the old SeqHound web services
- blmarker - biolegato for molecular markers. 'mbiolegato' will be a symbolic link to blmarker. A test version of blmarker is now available.
- bltree - biolegato for phylogenetic trees. 'tbiolegato' will be a symbolic link to bltree. A test version of bltree is now available.
- Modify bioLegato to work with the BL_DATA_DIR directory, rather than GDE_HELP_DIR.
- Move GDE environment variables for helper applications to BIRCH.properties (how do we handle platform-specific choices?)
- change birchdb documentation links from $tutorials/GDE to $tutorials/bioLegato
- change birchdb interface items from 'GDE' to 'biolegato' etc. Note: this may have implications for data items in lbirchdb.
- Need a better way to check for the presence of critical things like text editors, viewers etc during a new BIRCH installation, and set those to the defaults. Ideas:
- birchconfig should have a wizard for testing for presence of these programs and testing them. The final results get stored in the Birch.properties file.
- Change the admin/profile.source type files to read the value of variables such as GDE_TEXTEDIT from Birch.properties, rather than having them hard-coded. We would have to figure out how to work around the existing lines in local/admin files.
- modify scripts
- gde.treeoutput.csh is replaced by bltreeoutput.sh
- gde.helpviewer.csh is relaced by bl_help_viewer.sh
- dbsout.py - should call 'bldna', not 'gde'; We probably need to add a switch to say whether it calls 'bldna' or 'blprotein'
- fastaout.csh is replaced by fastaout.sh
- local GDEmenu items - We need to figure out the best way to convert over local GDE menu items. Should birchconfig try to automate this process? How much can we automate? How much has to be done by hand?