BIRCH

customdoc.py - Should always ignore changes in lines beginning with http, https, ftp etc. Otherwise, it breaks links to things like ftp:///ftp.cc.umanitoba.ca/psgendb..... Does htmldoc.py also need to be fixed? No.

Upgrade to Java 1.8

~~BioLegato 1.0.4 - recompiled using Java 1.8~~

~~Can flamingo and albacore be upgraded to Java 1.7?~~

Introducing blreads

~~Mechanism for setting max. CPU~~
~~General table functions~~
File/Directory functions
- ~~Delete~~
- ~~Unzip/bzunzip~~
- ~~cd - change directory~~
Sequence trimming and quality
- ~~trim_galore - rewrite scripts and PCD so that paired read files can be used as input.~~
- ~~fastq_pair - add binary and PCD menu~~
- Seqkit
  - For big files, seqkit stats can take a long time. Add email notification to this function. Also, add to the hints a note that as the # of CPUs increase, the load on RAM also increases, because SeqKit uses pigz to do decompression through an I/O stream for each file. It could be that things will go faster if we use a smaller number of CPUs. Some experimentation is in order.
Genome assembly and evaluation
- Pollux - automatically running FastQC on corrected reads doesn't work
Transcriptome assembly and evaluation
- SOAPdenovo-Trans - Installed for linux-x86_64. There are major problems involving static compilation and the inability to find libraries for osx-x86_64, and there appears to be no interest by the authors to support OSX. For now, SOAPdenovo-Trans will only be on linux-x86_64.
Tutorials
~~Hints - short help items in menus that tell you what to select, what is required~~
~~Can we get BioLegato overwrite function to work?~~
~~Hisat, Bowtie2, Cufflinks, StringTie - Current state of Tuxedo tools (Hisat supersedes TopHat)~~

~~http://www.ccb.jhu.edu/software/hisat/index.shtml~~

Testing

Dataset: Genome tutorial

	Linux			Mac OSX
	brassica (16 Gb)	flamingo	ccxx	peacock (8 Gb)	aliana (8 Gb)
Genome
Trimmomatic			+	+	+
trim_galore			+	+	+
pollux			+	+	+
SOAPdenovo2			+	NA	NA
ABySS			+	+	+
Spades			+	through K55	through K55
Quast			+	+	+

Dataset: Transcriptomics tutorial

	Linux			Mac OSX
	brassica (16 Gb)	flamingo	ccxx	peacock (8 Gb)	aliana (8 Gb)
Transcriptome
Trimmomatic			+	+
trim_galore			+	+	+
Rcorrector			+	+	+
SOAPdenovo-Trans			+	NA	NA
Trinity			+	NA	NA
RNASpades			+	through K49
transrate			+	+

Dataset: Differential expression tutorial

	Linux			Mac OSX
	brassica (16 Gb)	flamingo	ccxx	peacock (8 Gb)	aliana (8 Gb)
Differential Expression
gff2gtf			+	+
extract exons			+	+
extract splice sites			+	+
Hisat2-build			+	+
Hisat2			+	+
stringtie			+	+
stringtie merge			+	+
gffcompare			+	+
stringtie -B			+	+

BLAST/FASTA overhall

~~birchdb - some of the command line arguments for blastdbkit.py listed in the database are wrong eg. --addfiles should be --add. Fix these.~~

blpalign

~~None of the phylogeny programs work. They run, but we get an "unexpected end of file" error. WTF?~~

Other tasks, such as REFORM work, so it appears to be limited to phylogenies

all phylogeny programs work on CCL. Is this something specific to brassica?

~~Does this affect blnalign as well?~~

This is an old old bug leftover from GDE. The first part of the shell command for all the Phylip programs read as follows:

tr ""~"" ""-"" < %in1% | sed ""s/[\:\_]CDS/_/"" | readseq -a -f12 -pipe | sed ""s/ YF//1"" > %in1%.tmp;

the "| sed ""s/ YF//1" part would delete " YF" from any sequence in the Phylip alignment file. This would occur rarely ie. YF preceeded by a space, which is why it was not discovered until now. Anyway, the code has been fixed for all Phylip programs in blnalign and blpalign.