miga-base 1.2.15.1 → 1.2.15.3

data/utils/enveomics/LICENSE.txt

@@ -1,73 +0,0 @@
-Artistic License 2.0
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data/utils/enveomics/Makefile

@@ -1,52 +0,0 @@
-
-# Makefile for the Enve-omics collection
-# @update Oct 13 2013
-# @author Luis M. Rodriguez-R <lmrodriguez at gmail dot com>
-
-include globals.mk
-
-TEST=Tests
-enveomics_r=enveomics.R
-enveomics_r_v=enveomics.R_$(shell grep '^Version: ' enveomics.R/DESCRIPTION | perl -pe 's/.*: //')
-.PHONY: test install install-scripts install-r uninstall install-deps
-
-test: $(enveomics_r_v).tar.gz
-	@echo 
-	@echo Testing
-	cd $(TEST) && $(MAKE)
-	@echo 
-	@echo Testing $(enveomics_r)
-	$(R) CMD check --as-cran $(enveomics_r_v).tar.gz
-
-install: install-r install-scripts
-
-install-scripts:
-	[[ -d $(bindir)/lib ]] || mkdir $(bindir)/lib
-	ln -s $(foreach file,$(SCRIPTS),$(shell pwd)/$(file)) $(bindir)
-	ln -s $(shell pwd)/Scripts/lib/enveomics_rb $(bindir)/lib/
-	@echo
-	@echo Important note:
-	@echo This installation has simply created symbolic links to Scripts.
-	@echo If you need to move this folder, use uninstall/install afterwards.
-	@echo
-
-install-r:
-	$(R) CMD INSTALL $(enveomics_r)/
-
-uninstall:
-	-for file in $(foreach f,$(SCRIPTS),$(bindir)/$(notdir $f)) ; do \
-	   [[ -h $$file ]] && rm -r $$file ; \
-	done
-	-[[ -h $(bindir)/lib/enveomics_rb ]] && rm -r $(bindir)/lib/enveomics_rb
-	-$(R) CMD REMOVE $(enveomics_r)
-
-$(enveomics_r_v).tar.gz: install-deps
-	rm -f $(enveomics_r_v).tar.gz
-	./build_enveomics_r.bash
-	$(R) CMD build $(enveomics_r)/
-	$(MAKE) install-r
-
-install-deps: /usr/local/bin/brew /Library/TeX/texbin/pdflatex
-	pandoc -v %%>/dev/null || brew install pandoc
-	#qpdf -v %%>/dev/null || brew install qpdf
-	[[ -d /usr/local/opt/texinfo/bin ]] || brew install texinfo

data/utils/enveomics/Manifest/Tasks/aasubs.json

@@ -1,103 +0,0 @@
-{
-  "tasks": [
-    {
-      "task": "AAsubs.log2ratio.rb",
-      "description": ["Estimates the log2-ratio of different amino acids in",
-        "homologous sites using an AAsubs file (see BlastPairwise.AAsubs.pl).",
-        "It provides the point estimation (.obs file), the bootstrap of the",
-        "estimation (.boot file) and the null model based on label-permutation",
-        "(.null file)."],
-      "see_also": ["BlastPairwise.AAsubs.pl"],
-      "cite": [["Konstantinidis et al, 2009, AEM",
-        "http://dx.doi.org/10.1128%2FAEM.00473-09"]],
-      "help_arg": "--help",
-      "options": [
-        {
-          "opt": "--input",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": ["Input file in AAsubs format. It's a tab-delimited",
-            "table where each line corresponds to a substitution, the first",
-            "column corresponds to the compared protein IDs, the second",
-            "and third columns correspond to the AA on each protein, and the",
-            "fourth column indicates the length of the protein (not used by",
-            "this script."]
-        },
-        {
-          "opt": "--obs-file",
-          "arg": "out_file",
-          "description": ["Output file with the log2-ratios per amino acid.",
-            "By default, 'Input value'.obs."]
-        },
-        {
-          "opt": "--bootstrap-file",
-          "arg": "out_file",
-          "description": ["Output file with the bootstrap results of",
-            "log2-ratios per amino acid. By default, 'Input value'.boot."]
-        },
-        {
-          "opt": "--null-file",
-          "arg": "out_file",
-          "description": ["Output file with the permutation results of",
-            "log2-ratios per amino acid. By default, 'Input value'.null."]
-        },
-        {
-          "opt": "--overwrite",
-          "description": ["Overwrite existing files. By default, skip steps if",
-            "the files already exist."]
-        },
-        {
-          "opt": "--bootstraps",
-          "arg": "integer",
-          "default": 1000,
-          "description": "Number of bootstraps to run."
-        },
-        {
-          "opt": "--permutations",
-          "arg": "integer",
-          "default": 1000,
-          "description": "Number of permutations to run."
-        },
-        {
-          "opt": "--quiet",
-          "description": "Run quietly (no STDERR output)."
-        }
-      ]
-    },
-    {
-      "task": "BlastPairwise.AAsubs.pl",
-      "description": ["Counts the different AA substitutions in the best hit",
-        "blast alignments, from a BLASTP pairwise format output (-outfmt 0 in",
-        "BLAST+, -m 0 in legacy BLAST)."],
-      "see_also": ["AAsubs.log2ratio.rb"],
-      "cite": [["Konstantinidis et al, 2009, AEM",
-        "http://dx.doi.org/10.1128%2FAEM.00473-09"]],
-      "help_arg": "",
-      "options": [
-        {
-          "name": "Cigar char",
-          "arg": "select",
-          "values": ["+","_"],
-          "mandatory": true,
-          "description": ["Use '+' for similar substitutions, use '_' for non",
-            "similar substitutions."]
-        },
-        {
-          "name": "Blast M0",
-          "arg": "in_file",
-          "mandatory": true,
-          "description": "Blast in 'pairwise text' format (-outfmt/-m 0)."
-        },
-        ">",
-        {
-          "name": "AA subs",
-          "arg": "out_file",
-          "mandatory": true,
-          "description": ["A tab-delimited raw file with one substitution per",
-            "row and columns: (1) Name-of-query_Name-of-subject, (2)",
-            "AA-in-subject, (3) AA-in-query, (4) Total-Align-Length."]
-        }
-      ]
-    }
-  ]
-}