[Genabel-commits] r1834 - pkg/OmicABELnoMM/doc

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2014-10-14 09:08:27 +0200 (Tue, 14 Oct 2014)
New Revision: 1834

Modified:
   pkg/OmicABELnoMM/doc/howtocompile.txt
Log:
Used dos2unix to convert the newlines in the file from CR/LF to LF.


Modified: pkg/OmicABELnoMM/doc/howtocompile.txt
===================================================================
--- pkg/OmicABELnoMM/doc/howtocompile.txt	2014-10-08 09:02:15 UTC (rev 1833)
+++ pkg/OmicABELnoMM/doc/howtocompile.txt	2014-10-14 07:08:27 UTC (rev 1834)
@@ -1,20 +1,20 @@
 
 -------------------------Install BLAS----------------------------
 #STEP 1:
-#a) Install OPENBLAS:
-mkdir GWAS_PROJECT
-cd GWAS_PROJECT
+#a) Install OPENBLAS:
+mkdir GWAS_PROJECT
+cd GWAS_PROJECT
 
-#recommended to compile your own optimized blas! if not check Alternative Version at the end of the document
-#BLAS
-git clone git://github.com/xianyi/OpenBLAS
-cd OpenBLAS
-
-#make sure g++ its 4.8 or above!on rwth cluster module load gcc/4.8, choose 32 or 64 also
-make all HOSTCC=g++ FC=gfortran USE_OPENMP=1
-
-make install PREFIX="path_to_/OmicABELnoMM/libs/"
-
+#recommended to compile your own optimized blas! if not check Alternative Version at the end of the document
+#BLAS
+git clone git://github.com/xianyi/OpenBLAS
+cd OpenBLAS
+
+#make sure g++ its 4.8 or above!on rwth cluster module load gcc/4.8, choose 32 or 64 also
+make all HOSTCC=g++ FC=gfortran USE_OPENMP=1
+
+make install PREFIX="path_to_/OmicABELnoMM/libs/"
+
 ldconfig
 
 
@@ -40,8 +40,8 @@
 ---------------------------------#BLAS END----------------------------------------------------
 
 #STEP 2:
-
 
+
 ON the folder GWAS_PROJECT
 
 svn checkout svn://svn.r-forge.r-project.org/svnroot/genabel/pkg/OmicABELnoMM/
@@ -49,29 +49,29 @@
 cd OmicABELnoMM
 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:path_to_/OmicABELnoMM/libs/lib
 autoreconf -fi
-
+
 ./configure
 
 make
 
 make check
 
-#DONE
+#DONE
 
 ------------------------------Example--------------------------------
-#test it
+#test it
 ./omicabelnomm -c examples/XL --geno examples/XR -p examples/Y -o examples/B -n 2 -t 2
 
-#usage
-
-Must be included:
--c --cov filename		covariates in fv (no need for the .fvd/.fvi, both should have the same name!)
--g --geno filename		snps in fv (no need for the .fvd/.fvi, both should have the same name!)
--p --phe filename		traits in fv (no need for the .fvd/.fvi, both should have the same name!)
--o --out filename		file where betas will be written in fv (no need for the .fvd/.fvi, both should have the same name!)
-
-Optional:
--n --ngpred                     if the file in snp has a different model like direct data genotipic (2 columns per snp) specify -n 2, default is 1
+#usage
+
+Must be included:
+-c --cov filename		covariates in fv (no need for the .fvd/.fvi, both should have the same name!)
+-g --geno filename		snps in fv (no need for the .fvd/.fvi, both should have the same name!)
+-p --phe filename		traits in fv (no need for the .fvd/.fvi, both should have the same name!)
+-o --out filename		file where betas will be written in fv (no need for the .fvd/.fvi, both should have the same name!)
+
+Optional:
+-n --ngpred                     if the file in snp has a different model like direct data genotipic (2 columns per snp) specify -n 2, default is 1
 -t --thr			amount of threads to use, use = as the amount of physical processors in the system (max)