From c141be35e639a9318dff4493ffb42b782969ac38 Mon Sep 17 00:00:00 2001
From: Ben <ben.matern@gmail.com>
Date: Tue, 7 Mar 2017 09:30:30 +0100
Subject: [PATCH] relative links

---
 MakeExecutables.bat       |  8 ++------
 README.md                 | 11 ++++++-----
 Run_allele_submission.bat |  2 +-
 3 files changed, 9 insertions(+), 12 deletions(-)

diff --git a/MakeExecutables.bat b/MakeExecutables.bat
index 65f829c..db32d1d 100755
--- a/MakeExecutables.bat
+++ b/MakeExecutables.bat
@@ -20,12 +20,8 @@
 
 :: See the file README.MD for how to set up your anaconda environment.
 
-:: Please verify that your files are set up such that the files exist here::
-:: C:\MinIONScripts\AlleleSubmission\MakeExecutables.bat
-:: If that is a problem, Modify the spec file "AlleleSubInstallerOptions_Windows.spec" as your needs require.
-
-SET CodePath=C:\MUMCScripts\EMBL-HLA-Submission\src
-SET BinPath=C:\MUMCScripts\EMBL-HLA-Submission\bin
+SET CodePath=src
+SET BinPath=..\bin
 SET SpecFile=AlleleSubInstallerOptions_Windows.spec
 SET CondaEnvironment=AlleleSubEnvironment
 
diff --git a/README.md b/README.md
index 1be2884..70b453d 100644
--- a/README.md
+++ b/README.md
@@ -41,12 +41,12 @@ Run_allele_submission.bat
 ```
 
 ##Input Data
-Input data sequence consists of  
+Input data sequence must consist of  
 1) 5' UTR  
-2) An odd number of Exons, with an Even number of introns between them.  
+2) Any number of Exons, with an introns distributed between them.  
 3) 3' UTR
 
-Introns, Exons, and UTRs are to be specified using capital or lowercase letters.  
+Introns, Exons, and UTRs are to be distinguished using capital or lowercase nuclotide letters.  
 Exons are capital, while introns and UTRs are lowercase.
 
 Like this:  
@@ -54,7 +54,8 @@ fiveprimeutrEXONONEintrononeEXONTWOintrontwoEXONTHREEthreeprimeutr
 agctagctagctAGCTAGCtagctagctAGCTAGCtagctagctAGCTAGCTAgctagctagctag
 
 All spaces, tabs, and newlines are not interpreted by this program,  They are removed.
-If you wish, you may use those characters for more convenient visualization of splice sites:
+If you wish, you may use those characters for convenient visualization of splice sites, like this:
+
 agctagctagct  
 AGCTAGC  
 tagctagct  
@@ -64,7 +65,7 @@ AGCTAGCTA
 gctagctagctag  
 
 ##Output Data
-The resulting report is in the form of an EMBL HLA Novel Allele submission flatfile.  You can submit this to EMBL as a new allele.
+The resulting report is in the form of an EMBL HLA Novel Allele submission flatfile.  You can submit this to EMBL as a new HLA allele.
 
 ##For more information on EMBL's ENA format:  
 http://www.ebi.ac.uk/ena/submit/sequence-submission  
diff --git a/Run_allele_submission.bat b/Run_allele_submission.bat
index 24be771..a7152a8 100755
--- a/Run_allele_submission.bat
+++ b/Run_allele_submission.bat
@@ -17,5 +17,5 @@
 
 :: See the file README.MD for how to set up your anaconda environment.
 
-activate AlleleSubEnvironment && python AlleleSubmissionEMBL.py && deactivate
+activate AlleleSubEnvironment && cd src && python AlleleSubmissionEMBL.py && deactivate