README.md in bio-gemma-wrapper-0.0.1 vs README.md in bio-gemma-wrapper-0.92.2

@@ -28,11 +28,39 @@
 
 * A recent version of [GEMMA](https://github.com/genetics-statistics/GEMMA)
 * 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
 
     ./bin/gemma-wrapper --help
@@ -53,11 +81,11 @@
 ## Caching of K
 
 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 \
         -debug
 
@@ -69,11 +97,11 @@
 line switches passed into GEMMA as well as the contents of the files
 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 \
         -debug
 
@@ -85,11 +113,11 @@
 
 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 \
         -debug
 
@@ -100,22 +128,22 @@
 Recent versions of GEMMA have LOCO support for a single chromosome
 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 \
         -gk \
         -debug > K.json
 
 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 \
         -a test/data/input/BXD_snps.txt \
         -lmm 2 -maf 0.1 \
@@ -130,6 +158,6 @@
 The -k switch is injected automatically. Again output switches are not
 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.