moving things around

FlorianTrigodet · Aug 15, 2014 · cfc07f7 · cfc07f7
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diff --git a/Scripts/README b/Scripts/README
diff --git a/decompose → bin/decompose b/decompose → bin/decompose
diff --git a/entropy-analysis → bin/entropy-analysis b/entropy-analysis → bin/entropy-analysis
diff --git a/Scripts/R/bars-for-each-column.R → bin/o-bars-for-each-column.R b/Scripts/R/bars-for-each-column.R → bin/o-bars-for-each-column.R
diff --git a/Scripts/R/boxplots.R → bin/o-boxplots.R b/Scripts/R/boxplots.R → bin/o-boxplots.R
diff --git a/Scripts/R/cca-analysis.R → bin/o-cca-analysis.R b/Scripts/R/cca-analysis.R → bin/o-cca-analysis.R
diff --git a/Scripts/R/cluster-analysis.R → bin/o-cluster-analysis.R b/Scripts/R/cluster-analysis.R → bin/o-cluster-analysis.R
diff --git a/...o-create-GG-alignment-template-from-taxon → ...o-create-GG-alignment-template-from-taxon b/...o-create-GG-alignment-template-from-taxon → ...o-create-GG-alignment-template-from-taxon
diff --git a/Scripts/R/dist.R → bin/o-dist.R b/Scripts/R/dist.R → bin/o-dist.R
diff --git a/Scripts/o-fasta-length-distribution → bin/o-fasta-length-distribution b/Scripts/o-fasta-length-distribution → bin/o-fasta-length-distribution
diff --git a/Scripts/o-gen-dicts-for-qual-stats → bin/o-gen-dicts-for-qual-stats b/Scripts/o-gen-dicts-for-qual-stats → bin/o-gen-dicts-for-qual-stats
diff --git a/...o-gen-stackbar-with-sets-from-ENVIRONMENT → ...o-gen-stackbar-with-sets-from-ENVIRONMENT b/...o-gen-stackbar-with-sets-from-ENVIRONMENT → ...o-gen-stackbar-with-sets-from-ENVIRONMENT
diff --git a/Scripts/o-generate-consensus-from-alignment → bin/o-generate-consensus-from-alignment b/Scripts/o-generate-consensus-from-alignment → bin/o-generate-consensus-from-alignment
diff --git a/...o-generate-environment-from-matrix-counts → ...o-generate-environment-from-matrix-counts b/...o-generate-environment-from-matrix-counts → ...o-generate-environment-from-matrix-counts
diff --git a/Scripts/o-generate-exclusive-figures → bin/o-generate-exclusive-figures b/Scripts/o-generate-exclusive-figures → bin/o-generate-exclusive-figures
diff --git a/Scripts/o-generate-gephi-network-file → bin/o-generate-gephi-network-file b/Scripts/o-generate-gephi-network-file → bin/o-generate-gephi-network-file
diff --git a/Scripts/o-generate-matching-qual-file → bin/o-generate-matching-qual-file b/Scripts/o-generate-matching-qual-file → bin/o-generate-matching-qual-file
diff --git a/.../o-generate-matrix-files-from-ENVIRONMENT → bin/o-generate-matrix-files-from-ENVIRONMENT b/.../o-generate-matrix-files-from-ENVIRONMENT → bin/o-generate-matrix-files-from-ENVIRONMENT
diff --git a/Scripts/o-get-sample-info-from-fasta → bin/o-get-sample-info-from-fasta b/Scripts/o-get-sample-info-from-fasta → bin/o-get-sample-info-from-fasta
diff --git a/Scripts/R/heatmap.R → bin/o-heatmap.R b/Scripts/R/heatmap.R → bin/o-heatmap.R
diff --git a/Scripts/o-keep-or-remove-samples-from-fasta → bin/o-keep-or-remove-samples-from-fasta b/Scripts/o-keep-or-remove-samples-from-fasta → bin/o-keep-or-remove-samples-from-fasta
diff --git a/Scripts/R/lines-for-each-column.R → bin/o-lines-for-each-column.R b/Scripts/R/lines-for-each-column.R → bin/o-lines-for-each-column.R
diff --git a/Scripts/R/metaMDS-analysis-with-metadata.R → bin/o-metaMDS-analysis-with-metadata.R b/Scripts/R/metaMDS-analysis-with-metadata.R → bin/o-metaMDS-analysis-with-metadata.R
diff --git a/Scripts/R/metaMDS-analysis.R → bin/o-metaMDS-analysis.R b/Scripts/R/metaMDS-analysis.R → bin/o-metaMDS-analysis.R
diff --git a/Scripts/o-pad-with-gaps → bin/o-pad-with-gaps b/Scripts/o-pad-with-gaps → bin/o-pad-with-gaps
diff --git a/...s/o-populate-datasets-from-VAMPS-download → bin/o-populate-datasets-from-VAMPS-download b/...s/o-populate-datasets-from-VAMPS-download → bin/o-populate-datasets-from-VAMPS-download
diff --git a/Scripts/o-smart-trim-from-the-beginning → bin/o-smart-trim-from-the-beginning b/Scripts/o-smart-trim-from-the-beginning → bin/o-smart-trim-from-the-beginning
diff --git a/Scripts/R/stackbar.R → bin/o-stackbar.R b/Scripts/R/stackbar.R → bin/o-stackbar.R
diff --git a/Scripts/o-subsample-fasta-file → bin/o-subsample-fasta-file b/Scripts/o-subsample-fasta-file → bin/o-subsample-fasta-file
diff --git a/Scripts/o-subsample-matrix-file → bin/o-subsample-matrix-file b/Scripts/o-subsample-matrix-file → bin/o-subsample-matrix-file
diff --git a/Scripts/o-treat-homopolymer-regions → bin/o-treat-homopolymer-regions b/Scripts/o-treat-homopolymer-regions → bin/o-treat-homopolymer-regions
diff --git a/Scripts/o-trim → bin/o-trim b/Scripts/o-trim → bin/o-trim
diff --git a/...trim-uninformative-columns-from-alignment → ...trim-uninformative-columns-from-alignment b/...trim-uninformative-columns-from-alignment → ...trim-uninformative-columns-from-alignment
diff --git a/.../o-visualize-qual-scores-along-columns.py → bin/o-visualize-qual-scores-along-columns.py b/.../o-visualize-qual-scores-along-columns.py → bin/o-visualize-qual-scores-along-columns.py
diff --git a/oligotype → bin/oligotype b/oligotype → bin/oligotype