Apply fixes from upstream git repo. (#5178)

* Apply fixes from upstream git repo.

* Use perl-not-threaded, add summary and hash.

* Add jpeg-turbo as a runtime dependency.

* Update meta.yaml

* Update meta.yaml

* upgrade gnuplot version

* Update meta.yaml

Author: davebx

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; i<strlen(ascii_quality_scores); i++) {
+ 		pFASTX->quality[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 <limits.h>
+ 
+-#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)
+ 
+ 

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.'