Added fastq_utils recipe (#13473)

* Added fastq_utils recipe

* Remove noarch

* Attempt to fix curses error for Samtools following that recipe's example

* Attempt to resolve samtools compile issue

* Simplification and use of bam.h from Conda Samtools package

* Probably futile attempt at fix

* Try adding a conda build file

* Tidy up spacing

* Small futile tweaks

* Does this work to use newer GCC?

* Reinstate buld config, bump build

* Add compiler to host

* Revert "Add compiler to host"

This reverts commit 5c01e55.

* Replace gcc call with x86_64-apple-darwin13.4.0-clang

* sed the correct Makefile, use Make variable syntax

* Attempted fix for cannot find -lz

* Hopefully LDFLAGS is what's needed

* Okay, source package doesn't use LDFLAGS, use CFLAGS to pass options

* Try with older GCC

* Oh my god it works - tidy up

* Bumped runtime samtools to 1.9, removed legacy compiler requirement

recipes/fastq_utils/build.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+mkdir -p $PREFIX/bin
+
+export C_INCLUDE_PATH="${PREFIX}/include:${PREFIX}/include/bam"
+export CPP_INCLUDE_PATH="${PREFIX}/include"
+export CXX_INCLUDE_PATH="${PREFIX}/include"
+export LIBRARY_PATH="${PREFIX}/lib"
+export LD_LIBRARY_PATH="${PREFIX}/lib"
+
+# Compile and install. Replace gcc with $CC
+
+sed -i.bak "s/gcc/\$\(CC\)/g" src/Makefile
+export CFLAGS="$CFLAGS -L${PREFIX}/lib"
+make install
+
+# Copy executables into prefix
+
+cp bin/* $PREFIX/bin

recipes/fastq_utils/meta.yaml

@@ -0,0 +1,55 @@
+{% set version = "0.18.2" %}
+
+package:
+  name: fastq_utils
+  version: {{ version }}
+
+source:
+  url: https://github.com/nunofonseca/fastq_utils/archive/{{ version }}.tar.gz 
+  sha256: 0f0e554a0735eab68d2f4367e2b9071d71a94340b44318579e0a03b6850961e9
+
+build:
+  number: 1
+  skip: true  # [win32]
+
+requirements:
+  build:
+      - {{ compiler('c') }}
+      - make
+      - zlib
+  host:
+      - samtools ==0.1.19
+      - zlib
+      - ncurses
+  run:
+      - zlib
+      - samtools ==1.9
+
+# Note: these tools unhelpfully return exit codes of 1, so can't use their -h
+# arguments for testing
+
+test:
+    commands:
+        - which fastq_info
+        - which fastq_filterpair
+        - which fastq_filter_n
+        - which fastq_num_reads
+        - which fastq_trim_poly_at
+        - which fastq_pre_barcodes
+        - which bam_add_tags
+        - which bam_umi_count
+        - which fastq2bam
+        - which bam2fastq
+
+about:
+  home: https://github.com/nunofonseca/fastq_utils
+  dev_url: https://github.com/nunofonseca/fastq_utils
+  license: GPL-3
+  summary: Set of Linux utilities to validate and manipulate fastq files. It
+      also includes a set of programs to preprocess barcodes (namely UMIs,
+      cells and samples), add the barcodes as tags in BAM files and count UMIs. 
+  license_family: GPL
+
+extra:
+  recipe-maintainers:
+    - pinin4fjords