diff --git a/recipes/fastx_toolkit/fastx.patch b/recipes/fastx_toolkit/fastx.patch new file mode 100644 index 0000000000000..c3112d4fe70ed --- /dev/null +++ b/recipes/fastx_toolkit/fastx.patch @@ -0,0 +1,27 @@ +Common subdirectories: src/libfastx/.deps and src/libfastx/.deps +diff -Nau src/libfastx/fastx.c src/libfastx/fastx.c +--- src/libfastx/fastx.c 2014-01-05 16:10:49.000000000 -0500 ++++ src/libfastx/fastx.c 2017-07-11 09:49:25.609348867 -0400 +@@ -126,7 +126,7 @@ + + for (i=0; iquality[i] = (int) (ascii_quality_scores[i] - pFASTX->fastq_ascii_quality_offset ) ; +- if (pFASTX->quality[i] < -15 || pFASTX->quality[i] > 93) ++ if (pFASTX->quality[i] < MIN_QUALITY_VALUE || pFASTX->quality[i] > MAX_QUALITY_VALUE) + errx(1, "Invalid quality score value (char '%c' ord %d quality value %d) on line %lld", + ascii_quality_scores[i], ascii_quality_scores[i], + pFASTX->quality[i], pFASTX->input_line_number ); +diff -Nau src/libfastx/fastx.h src/libfastx/fastx.h +--- src/libfastx/fastx.h 2014-01-05 16:10:49.000000000 -0500 ++++ src/libfastx/fastx.h 2017-07-11 09:49:25.609348867 -0400 +@@ -25,8 +25,8 @@ + /* for PATH_MAX */ + #include + +-#define MIN_QUALITY_VALUE (-50) +-#define MAX_QUALITY_VALUE 50 ++#define MIN_QUALITY_VALUE (-15) ++#define MAX_QUALITY_VALUE 93 + #define QUALITY_VALUES_RANGE (MAX_QUALITY_VALUE-MIN_QUALITY_VALUE) + + diff --git a/recipes/fastx_toolkit/meta.yaml b/recipes/fastx_toolkit/meta.yaml index 7efc2c2ecf3eb..ebfc5f553dddb 100644 --- a/recipes/fastx_toolkit/meta.yaml +++ b/recipes/fastx_toolkit/meta.yaml @@ -5,10 +5,13 @@ package: source: url: https://github.com/agordon/fastx_toolkit/releases/download/0.0.14/fastx_toolkit-0.0.14.tar.bz2 fn: fastx_toolkit-0.0.14.tar.bz2 + md5: bf1993c898626bb147de3d6695c20b40 + patches: + - fastx.patch build: preserve_egg_dir: True - number: 3 + number: 4 skip: False requirements: @@ -24,13 +27,11 @@ requirements: - cython - nose - libgtextutils - - gnuplot - - libgd >=2.1.1post 1 - - perl-threaded + - gnuplot >=5.0.5 + - perl - perl-perlio-gzip - - perl-gd >=2.5.6 2 + - perl-gd - perl-gdgraph-histogram - #- pkg-config test: commands: @@ -40,3 +41,20 @@ test: about: home: https://github.com/agordon/fastx_toolkit license: AGPL + summary: 'The FASTX-Toolkit is a collection of command line tools for + Short-Reads FASTA/FASTQ files preprocessing. + + Next-Generation sequencing machines usually produce FASTA or FASTQ files, + containing multiple short-reads sequences (possibly with quality + information). + + The main processing of such FASTA/FASTQ files is mapping (aka aligning) the + sequences to reference genomes or other databases using specialized + programs. Example of such mapping programs are: Blat, SHRiMP, LastZ, MAQ + and many many others. + + However, it is sometimes more productive to preprocess the FASTA/FASTQ files + before mapping the sequences to the genome - manipulating the sequences to + produce better mapping results. + + The FASTX-Toolkit tools perform some of these preprocessing tasks.'