Enveomics collection added as submodule

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "utils/enveomics"]
+	path = utils/enveomics
+	url = https://github.com/lmrodriguezr/enveomics.git

miga-base.gemspec

@@ -19,7 +19,7 @@ Gem::Specification.new do |s|
   # Files
   s.files = Dir[
     "lib/**/*.rb", "test/**/*.rb", "lib/miga/_data/**/*",
-    "scripts/*.bash", "utils/*", "bin/*", "actions/*",
+    "scripts/*.bash", "utils/**/*", "bin/*", "actions/*",
     "Gemfile", "Rakefile", "README.md", "LICENSE"
   ]
   s.executables	<< "miga"

scripts/trimmed_fasta.bash

@@ -21,13 +21,14 @@ for sis in 1 2 ; do
 done
 
 # FastQ -> FastA
-FastQ.toFastA.awk < "../02.trimmed_reads/$b.1.clipped.fastq" > "$b.1.fasta"
+FQ2A="$MIGA/utils/enveomics/Scripts/FastQ.toFastA.awk"
+awk -f "$FQ2A" < "../02.trimmed_reads/$b.1.clipped.fastq" > "$b.1.fasta"
 if [[ -e "../02.trimmed_reads/$b.2.clipped.fastq" ]] ; then
-  FastQ.toFastA.awk < "../02.trimmed_reads/$b.2.clipped.fastq" > "$b.2.fasta"
+  awk -f "$FQ2A" < "../02.trimmed_reads/$b.2.clipped.fastq" > "$b.2.fasta"
   FastA.interpose.pl "$b.CoupledReads.fa" "$b".[12].fasta
   gzip -9 -f "$b.2.fasta"
   gzip -9 -f "$b.1.fasta"
-  FastQ.toFastA.awk < "../02.trimmed_reads/$b".[12].clipped.single.fastq \
+  awk -f "$FQ2A" < "../02.trimmed_reads/$b".[12].clipped.single.fastq \
     > "$b.SingleReads.fa"
   gzip -9 -f "$b.SingleReads.fa"
 else

utils/requirements.txt

@@ -1,19 +1,17 @@
-Software		Test executable		Website								Notes
---------		---------------		-------								-----
-Enve-omics scripts	FastQ.tag.rb		http://github.com/lmrodriguezr/enveomics			All the collection must be present
-SolexaQA++		SolexaQA++		http://solexaqa.sourceforge.net					Required version: v3.1.3+
-Scythe			scythe			https://github.com/vsbuffalo/scythe				Required version: 0.991+
-FastQC			fastqc			http://www.bioinformatics.babraham.ac.uk/projects/fastqc
-IDBA			idba_ud			http://i.cs.hku.hk/~alse/hkubrg/projects/idba
-Prodigal		prodigal		http://prodigal.ornl.gov
-HMMer 3.0+		hmmsearch		http://hmmer.janelia.org/software
-NCBI BLAST+		blastp			ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST
-R			R			http://www.r-project.org/
-SQLite3			sqlite3			https://www.sqlite.org/
-RAxML (pthreads)	raxmlHPC-PTHREADS	http://sco.h-its.org/exelixis/web/software/raxml/index.html
-MCL			mcl			http://micans.org/mcl/
-DIAMOND			diamond			http://ab.inf.uni-tuebingen.de/software/diamond			Required version: v0.7.9+
-MyTaxa			MyTaxa			http://enve-omics.ce.gatech.edu/mytaxa				The folder must contain the db and utils dirs, and the AllGenomes.faa BLAST database
-Krona			ktImportText		https://github.com/marbl/Krona/wiki
-Barrnap			barrnap			http://www.vicbioinformatics.com/software.barrnap.shtml
-bedtools		bedtools		http://bedtools.readthedocs.org/en/latest/
+Software	Test exec	Website								Notes
+--------	---------	-------								-----
+R		R		http://www.r-project.org/
+SQLite3		sqlite3		https://www.sqlite.org/
+NCBI BLAST+	blastp		ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST
+HMMer 3.0+	hmmsearch	http://hmmer.janelia.org/software
+Bedtools	bedtools	http://bedtools.readthedocs.org/en/latest/
+Prodigal	prodigal	http://prodigal.ornl.gov
+IDBA		idba_ud		http://i.cs.hku.hk/~alse/hkubrg/projects/idba
+MCL		mcl		http://micans.org/mcl/
+Barrnap		barrnap		http://www.vicbioinformatics.com/software.barrnap.shtml
+Scythe		scythe		https://github.com/vsbuffalo/scythe				Required version: 0.991+
+FastQC		fastqc		http://www.bioinformatics.babraham.ac.uk/projects/fastqc
+SolexaQA++	SolexaQA++	http://solexaqa.sourceforge.net					Required version: v3.1.3+
+DIAMOND (opt)	diamond		http://ab.inf.uni-tuebingen.de/software/diamond			Required version: v0.7.9+
+MyTaxa (opt)	MyTaxa		http://enve-omics.ce.gatech.edu/mytaxa				The folder must contain the db and utils dirs, and the AllGenomes.faa.dmnd database
+Krona (opt)	ktImportText	https://github.com/marbl/Krona/wiki