From aa057b794b56ebe97c9f1393fc6b09f1d74225a7 Mon Sep 17 00:00:00 2001
From: sdyy1990 <sdyy1990@gmail.com>
Date: Mon, 6 Nov 2017 13:42:51 -0500
Subject: [PATCH] update readme

---
 README.md                          | 4 ++--
 build.sh => compile.sh             | 0
 buildUKYDLX.sh => compileUKYDLX.sh | 0
 genBuildFromJellyfishKmers.sh      | 6 +++---
 genExample.sh                      | 2 +-
 5 files changed, 6 insertions(+), 6 deletions(-)
 rename build.sh => compile.sh (100%)
 rename buildUKYDLX.sh => compileUKYDLX.sh (100%)

diff --git a/README.md b/README.md
index 9ab1a47..522c42d 100644
--- a/README.md
+++ b/README.md
@@ -11,7 +11,7 @@ libz >= 1.2.3
 ```
 To compile the SeqOthello tool chain, decompress the source code and execute the following commands in the source folder.
 ```
-./build.sh
+./compile.sh
 ```
 Then you can find the compile resutls in the ```build/bin``` folder. 
 
@@ -56,4 +56,4 @@ Use the following command to start a server on the machine, (e.g., on TCP port 3
 ```build/bin/Query --map-folder=out/ --start-server-port 3322```
 
 In another terminal, run the Client program.
-```build/bin/Client --transcript=kmer/test.fa --coverage --output=result --port=3333```
\ No newline at end of file
+```build/bin/Client --transcript=kmer/test.fa --coverage --output=result --port=3333```
diff --git a/build.sh b/compile.sh
similarity index 100%
rename from build.sh
rename to compile.sh
diff --git a/buildUKYDLX.sh b/compileUKYDLX.sh
similarity index 100%
rename from buildUKYDLX.sh
rename to compileUKYDLX.sh
diff --git a/genBuildFromJellyfishKmers.sh b/genBuildFromJellyfishKmers.sh
index 876d80b..fb1348d 100755
--- a/genBuildFromJellyfishKmers.sh
+++ b/genBuildFromJellyfishKmers.sh
@@ -33,7 +33,7 @@ TEMP_FOLDER="${INPUT:-`pwd`}"
 
 if [ ! -d ${TEMP_FOLDER}/bin ]; then 
     echo 'folder' ${TEMP_FOLDER}'/bin/ does not exist, creating.'
-    mkdir -p mkdir -p ${TEMP_FOLDER}/bin
+    mkdir -p ${TEMP_FOLDER}/bin
 fi
 
 
@@ -79,7 +79,7 @@ echo '        These group description files are' ${TEMP_FOLDER}/${BINARY_LIST_PR
 
 if [ ! -d ${TEMP_FOLDER}/grp ]; then 
     echo 'folder' ${TEMP_FOLDER}'/grp/ does not exist, creating.'
-    mkdir -p mkdir -p ${TEMP_FOLDER}/grp
+    mkdir  -p ${TEMP_FOLDER}/grp
 fi
 
 MAKE_GROUP=MakeGroup.sh
@@ -114,7 +114,7 @@ EXPORT_FOLDER="${INPUT:-$EXPORT_FOLDER_DEFAULT}"
 
 if [ ! -d ${EXPORT_FOLDER} ]; then 
     echo 'folder' ${EXPORT_FOLDER} 'does not exist, creating.'
-    mkdir -p mkdir -p ${EXPORT_FOLDER}
+    mkdir -p ${EXPORT_FOLDER}
 fi
 
 while [ ! -d ${KMER_PATH} ]; do 
diff --git a/genExample.sh b/genExample.sh
index ecc0040..108a296 100755
--- a/genExample.sh
+++ b/genExample.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 mkdir -p kmer
 cd kmer
-../build/test/datagen -f 182 -k 15300 > genlog
+../build0/test/datagen -f 182 -k 15300 > genlog
 echo '>xxxxxxxxx|yyyyyyyyyy' > test.fa
 tail -n 1 genlog >> test.fa
 ls -m1 *.Kmer > flist