From d58beeee56d2ee9b6b4f0f7eb2396d0337aa85fb Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 19 Nov 2014 12:38:55 -0500 Subject: [PATCH 1/2] smarter about path finding --- bwakit/run-bwamem | 1 + 1 file changed, 1 insertion(+) diff --git a/bwakit/run-bwamem b/bwakit/run-bwamem index 4c75de9..1b40be2 100755 --- a/bwakit/run-bwamem +++ b/bwakit/run-bwamem @@ -55,6 +55,7 @@ my $idx = $ARGV[0]; my $exepath = $0 =~/^\S+\/[^\/\s]+/? $0 : &which($0); my $root = $0 =~/^(\S+)\/[^\/\s]+/? $1 : undef; +$root = $exepath =~/^(\S+)\/[^\/\s]+/? $1 : undef if !defined($root); die "ERROR: failed to locate the 'bwa.kit' directory\n" if !defined($root); die("ERROR: failed to locate the BWA index. Please run '$root/bwa index -p $idx ref.fa'.\n") From 6609bafa175466c76fb57b441e50321d4db3790b Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 19 Nov 2014 12:45:21 -0500 Subject: [PATCH 2/2] moved directory structure to this README There are too many README files... --- bwakit/README.md | 43 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 43 insertions(+) diff --git a/bwakit/README.md b/bwakit/README.md index 5dcc32f..f16e74d 100644 --- a/bwakit/README.md +++ b/bwakit/README.md @@ -1,3 +1,5 @@ +## Introduction + Bwakit is a self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping. In addition to the basic mapping functionality implemented in bwa, bwakit is able to generate @@ -42,6 +44,47 @@ Bwakit can be [downloaded here][res]. It is only available to x86_64-linux. The scripts in the package are available in the [bwa/bwakit][kit] directory. Packaging is done manually for now. +## Contents +``` +bwa.kit +|-- README.md This README file. +|-- run-bwamem *Entry script* for the entire mapping pipeline. +|-- bwa *BWA binary* +|-- k8 Interpretor for *.js scripts. +|-- bwa-postalt.js Post-process alignments to ALT contigs/decoys/HLA genes. +|-- htsbox Used by run-bwamem for shuffling BAMs and BAM=>FASTQ. +|-- samblaster MarkDuplicates for reads from the same library. v0.1.20 +|-- samtools SAMtools for sorting and SAM=>BAM conversion. v1.1 +|-- seqtk For FASTQ manipulation. +|-- trimadap Trim Illumina PE sequencing adapters. +| +|-- run-gen-ref *Entry script* for generating human reference genomes. +|-- resource-GRCh38 Resources for generating GRCh38 +| |-- hs38d6-decoy.nt.anno Top decoy-to-nt hits. Not used by any scripts. +| |-- hs38d6-decoy.rm.out RepeatMasker report. Not used. +| |-- hs38d6-extra.fa Decoy and HLA gene sequences. Used by run-gen-ref. +| `-- hs38d6.fa.alt ALT-to-GRCh38 alignment. Used by run-gen-ref. +| +|-- run-HLA HLA typing for sequences extracted by bwa-postalt.js. +|-- typeHLA.sh Type one HLA-gene. Called by run-HLA. +|-- typeHLA.js HLA typing from exon-to-contig alignment. Used by typeHLA.sh. +|-- typeHLA-selctg.js Select contigs overlapping HLA exons. Used by typeHLA.sh. +|-- fermi2.pl Fermi2 wrapper. Used by typeHLA.sh for de novo assembly. +|-- fermi2 Fermi2 binary. Used by fermi2.pl. +|-- ropebwt2 RopeBWT2 binary. Used by fermi2.pl. +|-- resource-human-HLA Resources for HLA typing +| |-- HLA-ALT-exons.bed Exonic regions of HLA ALT contigs. Used by typeHLA.sh. +| |-- HLA-CDS.fa CDS of HLA-{A,B,C,DQA1,DQB1,DRB1} genes from IMGT/HLA-3.18.0. +| |-- HLA-ALT-type.txt HLA types for each HLA ALT contig. Not used. +| `-- HLA-ALT-idx BWA indices of each HLA ALT contig. Used by typeHLA.sh +| `-- (...) +| +`-- doc BWA documentations + |-- bwa.1 Manpage + |-- NEWS.md Release Notes + |-- README.md GitHub README page + `-- README-alt.md Documentation for ALT mapping +``` [res]: https://sourceforge.net/projects/bio-bwa/files/bwakit [sb]: https://github.com/GregoryFaust/samblaster