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Enveomics collection added as submodule

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lmrodriguezr committed Jun 4, 2017
1 parent f6a1c6a commit 4b7a53e0f4f83432b558d0b9825779ddee42407a
@@ -0,0 +1,3 @@
[submodule "utils/enveomics"]
path = utils/enveomics
url = https://github.com/lmrodriguezr/enveomics.git
@@ -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"
@@ -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
Submodule enveomics added at 64607e
0 utils/index_metadata.rb 100644 → 100755
No changes.
0 utils/plot-taxdist.R 100644 → 100755
No changes.
@@ -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

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