bio-gemma-wrapper 0.0.1 → 0.92.2

checksums.yaml

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data/README.md

@@ -30,7 +30,35 @@ Prerequisites are
 * Standard [Ruby >2.0 ](https://www.ruby-lang.org/en/) which comes on
   almost all Linux systems
 
-Fetch a [release](https://github.com/genetics-statistics/gemma-wrapper/releases) of
+gemma-wrapper comes as a Ruby [gem](https://rubygems.org/gems/bio-gemma-wrapper) and
+can be installed with
+
+    gem install bio-gemma-wrapper
+
+Invoke the tool with
+
+    gemma-wrapper --help
+
+and it will render
+
+```
+Usage: gemma-wrapper [options] -- [gemma-options]
+        --loco [x,y,1,2,3...]        Run full LOCO
+        --input filen                JSON input variables (used for LOCO)
+        --cache-dir path             Use a cache directory
+        --json                       Create output file in JSON format
+        --force                      Force computation
+        --q, --quiet                 Run quietly
+    -v, --verbose                    Run verbosely
+        --debug                      Show debug messages and keep intermediate output
+        --                           Anything after gets passed to GEMMA
+
+    -h, --help                       display this help and exit
+```
+
+Alternatively, fetch a
+[release](https://github.com/genetics-statistics/gemma-wrapper/releases)
+of
 [gemma-wrapper](https://github.com/genetics-statistics/gemma-wrapper)
 
 Unpack it and run the tool as
@@ -55,7 +83,7 @@ prints the GEMMA help
 To compute K run the following command from the source directory (so
 the data files are found):
 
-    ./bin/gemma-wrapper -- \
+    gemma-wrapper -- \
         -g test/data/input/BXD_geno.txt.gz \
         -p test/data/input/BXD_pheno.txt \
         -gk \
@@ -71,7 +99,7 @@ passed in (here the genotype and phenotype files).
 
 You can also get JSON output on STDOUT by providing the --json switch
 
-    ./bin/gemma-wrapper --json -- \
+    gemma-wrapper --json -- \
         -g test/data/input/BXD_geno.txt.gz \
         -p test/data/input/BXD_pheno.txt \
         -gk \
@@ -87,7 +115,7 @@ Note that GEMMA's -o (output) and --outdir switches should not be
 used. gemma-wrapper stores the cached matrices in TMPDIR by
 default. If you want something else provide a --cache-dir, e.g.
 
-    ./bin/gemma-wrapper --cache-dir ~/.gemma-cache -- \
+    gemma-wrapper --cache-dir ~/.gemma-cache -- \
         -g test/data/input/BXD_geno.txt.gz \
         -p test/data/input/BXD_pheno.txt \
         -gk \
@@ -102,8 +130,8 @@ using the -loco switch (for supported formats check
 https://github.com/genetics-statistics/GEMMA/issues/46). To loop all
 chromosomes first create all K's with
 
-    ./bin/gemma-wrapper --json \
-        --loco 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y -- \
+    gemma-wrapper --json \
+        --loco 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X -- \
         -g test/data/input/BXD_geno.txt.gz \
         -p test/data/input/BXD_pheno.txt \
         -a test/data/input/BXD_snps.txt \
@@ -113,7 +141,7 @@ chromosomes first create all K's with
 and next run the LMM's using the K's captured in K.json using the --input
 switch
 
-    ./bin/gemma-wrapper --json --loco --input K.json -- \
+    gemma-wrapper --json --loco --input K.json -- \
         -g test/data/input/BXD_geno.txt.gz \
         -p test/data/input/BXD_pheno.txt \
         -c test/data/input/BXD_covariates2.txt \
@@ -132,4 +160,4 @@ allowed (-o, -outdir)
 
 ## Copyright
 
-Copyright (c) 2017 Pjotr Prins. See LICENSE.txt for further details.
+Copyright (c) 2017 Pjotr Prins. See [LICENSE.txt](LICENSE.txt) for further details.

data/VERSION

@@ -1 +1 @@
-0.0.1
+0.92.2

data/bin/gemma-wrapper

@@ -6,7 +6,37 @@
 #
 # Copyright (C) 2017 Pjotr Prins <pjotr.prins@thebird.nl>
 
-USAGE = "GEMMA K handler"
+USAGE = "GEMMA wrapper example:
+
+    Simple caching of K computation with
+
+      gemma-wrapper -- \\
+        -g test/data/input/BXD_geno.txt.gz \\
+        -p test/data/input/BXD_pheno.txt \\
+        -gk
+
+    LOCO K computation with caching and JSON output
+
+      gemma-wrapper --json \\
+        --loco 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X -- \\
+        -g test/data/input/BXD_geno.txt.gz \\
+        -p test/data/input/BXD_pheno.txt \\
+        -a test/data/input/BXD_snps.txt \\
+        -gk -debug > K.json
+
+    LMM's using the K's captured in K.json using the --input switch
+
+      gemma-wrapper --json --loco --input K.json -- \\
+        -g test/data/input/BXD_geno.txt.gz \\
+        -p test/data/input/BXD_pheno.txt \\
+        -c test/data/input/BXD_covariates2.txt \\
+        -a test/data/input/BXD_snps.txt \\
+        -lmm 2 -maf 0.1 \\
+        -debug > GWA.json
+
+"
+GEMMA_V_MAJOR = 97
+GEMMA_V_MINOR = 2
 
 basepath = File.dirname(File.dirname(__FILE__))
 $: << File.join(basepath,'lib')
@@ -126,6 +156,18 @@ GEMMA_K_VERSION=version
 GEMMA_K_BANNER = "gemma-wrapper #{version} (Ruby #{RUBY_VERSION}) by Pjotr Prins 2017\n"
 info.call GEMMA_K_BANNER
 
+# Check gemma version
+GEMMA_COMMAND=options[:gemma_command]
+gemma_version_header = `#{GEMMA_COMMAND}`.split("\n").grep(/Version/)[0].strip
+info.call "Using GEMMA ",gemma_version_header,"\n"
+gemma_version = gemma_version_header.split(/[,\s]+/)[1]
+v_version, v_major, v_minor = gemma_version.split(".")
+
+error.call "GEMMA version is out of date. Update GEMMA to 0.#{GEMMA_V_MAJOR}.#{GEMMA_V_MINOR}!" if v_major.to_i < GEMMA_V_MAJOR or (v_major.to_i == GEMMA_V_MAJOR and (v_minor == nil or v_minor.to_i < GEMMA_V_MINOR))
+
+options[:gemma_version_header] = gemma_version_header
+options[:gemma_version] = gemma_version
+
 if options[:show_help] or gemma_args == nil
   print opts
   print USAGE
@@ -166,15 +208,6 @@ gemma_args << '-outdir'
 gemma_args << options[:cache_dir]
 GEMMA_ARGS = gemma_args
 
-# Check gemma version
-GEMMA_COMMAND=options[:gemma_command]
-gemma_version_header = `#{GEMMA_COMMAND}`.split("\n").grep(/Version/)[0].strip
-info.call "Using GEMMA ",gemma_version_header,"\n"
-gemma_version = gemma_version_header.split(/[,\s]+/)[1]
-
-options[:gemma_version_header] = gemma_version_header
-options[:gemma_version] = gemma_version
-
 debug.call "Options: ",options,"\n" if !options[:quiet]
 
 invoke_gemma = lambda do |extra_args, cache_hit = false|

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-gemma-wrapper
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.92.2
 platform: ruby
 authors:
 - Pjotr Prins
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-08-29 00:00:00.000000000 Z
+date: 2017-09-03 00:00:00.000000000 Z
 dependencies: []
 description: GEMMA wrapper caches K between runs with LOCO support
 email: pjotr.public01@thebird.nl
@@ -43,7 +43,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.8
+rubygems_version: 2.5.1
 signing_key: 
 specification_version: 4
 summary: Cache GEMMA with LOCO