From d07fdd1e335aee154373c416eafab589ce4bf9a6 Mon Sep 17 00:00:00 2001
From: lfaino <M3Fw3K2h>
Date: Fri, 2 Nov 2018 11:55:01 +0100
Subject: [PATCH 1/2] V2.0

---
 INSTALL.md | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/INSTALL.md b/INSTALL.md
index b5fcb126..a3aa0841 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -55,12 +55,12 @@ source command.
 
 ```bash
 singularity pull --name mysql.simg shub://ISU-HPC/mysql
-wget -O ~/.my.cnf https://raw.githubusercontent.com/lfaino/LoReAn/dev/third_party/conf_files/my.cnf 
-wget -O ~/.mysqlrootpw https://raw.githubusercontent.com/lfaino/LoReAn/dev/third_party/conf_files/mysqlrootpw
+wget -O ~/.my.cnf https://raw.githubusercontent.com/lfaino/LoReAn/master/third_party/conf_files/my.cnf 
+wget -O ~/.mysqlrootpw https://raw.githubusercontent.com/lfaino/LoReAn/master/third_party/conf_files/mysqlrootpw
 mkdir -p ${HOME}/mysql/var/lib/mysql ${HOME}/mysql/run/mysqld
 singularity instance.start --bind ${HOME} --bind ${HOME}/mysql/var/lib/mysql/:/var/lib/mysql --bind ${HOME}/mysql/run/mysqld:/run/mysqld ./mysql.simg mysql
 singularity run instance://mysql
-singularity shell --bind ${HOME}/mysql/run/mysqld:/run/mysqld/  docker://lfaino/lorean:iprscan_rpMask
+singularity shell --bind ${HOME}/mysql/run/mysqld:/run/mysqld/  docker://lfaino/lorean
 cat ~/.bashrc /opt/LoReAn/third_party/conf_files/pathToExport.txt  > ~/.bashrc.lorean
 source ~/.bashrc.lorean
 cp -r /opt/LoReAn/third_party/software/augustus/ ~/
@@ -128,7 +128,7 @@ https://docs.docker.com/engine/installation/
 
 After Docker installation, you can download  LoReAn by using:
 ```bash
-docker run -it --rm -v $PWD:/data lfaino/lorean:iprscan_rpMask createUser.py $USER $UID 
+docker run -it --rm -v $PWD:/data lfaino/lorean createUser.py $USER $UID 
 ```
 
 At this point, run

From dff3fdf7693353ca94eb947d46c38f7d74e908be Mon Sep 17 00:00:00 2001
From: lfaino <M3Fw3K2h>
Date: Fri, 2 Nov 2018 12:06:24 +0100
Subject: [PATCH 2/2] remove Files

---
 filetypes.xml | 11 -----------
 ignore.xml    | 33 ---------------------------------
 perl5.xml     |  6 ------
 3 files changed, 50 deletions(-)
 delete mode 100644 filetypes.xml
 delete mode 100644 ignore.xml
 delete mode 100644 perl5.xml

diff --git a/filetypes.xml b/filetypes.xml
deleted file mode 100644
index 4b9492da..00000000
--- a/filetypes.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<application>
-  <component name="FileTypeManager" version="17">
-    <extensionMap>
-      <mapping pattern="Dockerfile_1" type="PLAIN_TEXT" />
-      <mapping pattern="mysqlrootpw" type="PLAIN_TEXT" />
-      <mapping ext="cnf" type="PLAIN_TEXT" />
-      <mapping ext="bck" type="PLAIN_TEXT" />
-      <mapping ext="gff" type="PLAIN_TEXT" />
-    </extensionMap>
-  </component>
-</application>
\ No newline at end of file
diff --git a/ignore.xml b/ignore.xml
deleted file mode 100644
index 28260d90..00000000
--- a/ignore.xml
+++ /dev/null
@@ -1,33 +0,0 @@
-<application>
-  <component name="IgnoreSettings" missingGitignore="true" ignoredFileStatus="true" outerIgnoreRules="true" outerIgnoreWrapperHeight="300" version="3.0.0.182" starredTemplates="" unignoreActions="true" hideIgnoredFiles="false" informTrackedIgnored="true" notifyIgnoredEditing="true">
-    <languages>
-      <language id="Bazaar" NEW_FILE="true" ENABLE="true" />
-      <language id="CloudFoundry" NEW_FILE="true" ENABLE="false" />
-      <language id="Chef" NEW_FILE="true" ENABLE="false" />
-      <language id="Cvs" NEW_FILE="true" ENABLE="true" />
-      <language id="Darcs" NEW_FILE="true" ENABLE="true" />
-      <language id="Docker" NEW_FILE="true" ENABLE="false" />
-      <language id="ElasticBeanstalk" NEW_FILE="true" ENABLE="false" />
-      <language id="ESLint" NEW_FILE="true" ENABLE="false" />
-      <language id="Floobits" NEW_FILE="true" ENABLE="false" />
-      <language id="Fossil" NEW_FILE="true" ENABLE="true" />
-      <language id="Git" NEW_FILE="true" ENABLE="true" />
-      <language id="Git exclude" NEW_FILE="true" ENABLE="true" />
-      <language id="Kubernetes Helm" NEW_FILE="true" ENABLE="false" />
-      <language id="Jetpack" NEW_FILE="true" ENABLE="false" />
-      <language id="JSHint" NEW_FILE="true" ENABLE="false" />
-      <language id="Mercurial" NEW_FILE="true" ENABLE="true" />
-      <language id="Monotone" NEW_FILE="true" ENABLE="true" />
-      <language id="Nodemon" NEW_FILE="true" ENABLE="false" />
-      <language id="Npm" NEW_FILE="true" ENABLE="false" />
-      <language id="Perforce" NEW_FILE="true" ENABLE="true" />
-      <language id="Prettier" NEW_FILE="true" ENABLE="false" />
-      <language id="StyleLint" NEW_FILE="true" ENABLE="false" />
-      <language id="Stylint" NEW_FILE="true" ENABLE="false" />
-      <language id="Swagger Codegen" NEW_FILE="true" ENABLE="false" />
-      <language id="Team Foundation" NEW_FILE="true" ENABLE="true" />
-      <language id="Up" NEW_FILE="true" ENABLE="false" />
-    </languages>
-    <userTemplates />
-  </component>
-</application>
\ No newline at end of file
diff --git a/perl5.xml b/perl5.xml
deleted file mode 100644
index 68ef799f..00000000
--- a/perl5.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<application>
-  <component name="Perl5ApplicationSettings">
-    <option name="pluginVersion" value="2018.2.1" />
-    <option name="popupShown" value="true" />
-  </component>
-</application>
\ No newline at end of file