From 44c7a23ab2bdcaa7652035f8817637709c136ddd Mon Sep 17 00:00:00 2001
From: Lmercadom <42242797+Lmercadom@users.noreply.github.com>
Date: Tue, 20 Nov 2018 15:00:14 -0500
Subject: [PATCH 1/2] Update run-bedtobeddb.sh

---
 scripts/run-bedtobeddb.sh | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/scripts/run-bedtobeddb.sh b/scripts/run-bedtobeddb.sh
index 8a97610..4b226ed 100644
--- a/scripts/run-bedtobeddb.sh
+++ b/scripts/run-bedtobeddb.sh
@@ -7,8 +7,7 @@ ASSEMBLY=$2
 OUTDIR=$3
 
 FILE_BASE=$(basename $INPUT)
-FILE_NAME=${FILE_BASE%.*}
-echo $FILE_NAME
+FILE_NAME=${FILE_BASE%%.*}
 
 mkfifo pp
 
@@ -20,7 +19,6 @@ fi
 gunzip -c $INPUT > pp.bed
 
 outputfile="$OUTDIR/$FILE_NAME.beddb"
-echo $outputfile
 
 clodius aggregate bedfile \
   --assembly $ASSEMBLY -o $outputfile \

From ff1ed904c33af9312bcfcbc7285ddc065468a48c Mon Sep 17 00:00:00 2001
From: Lmercadom <42242797+Lmercadom@users.noreply.github.com>
Date: Thu, 23 May 2019 10:55:20 -0400
Subject: [PATCH 2/2] Update README.md

---
 README.md | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 47f1e3f..776dc5b 100644
--- a/README.md
+++ b/README.md
@@ -48,7 +48,7 @@ Sample data files that can be used for testing the tools are included in the `sa
 
 ## Tool wrappers
 
-Tool wrappers are under the `scripts` directory and follow naming conventions `run-xx.sh`. These wrappers are copied to the docker image at built time and may be used as a single step in a workflow. (Current version has no tool wrappers)
+Tool wrappers are under the `scripts` directory and follow naming conventions `run-xx.sh`. These wrappers are copied to the docker image at built time and may be used as a single step in a workflow.
 
 ```
 # default
@@ -60,3 +60,17 @@ docker run 4dndcic/4dn-bedtobeddb <run-xx.sh> <arg1> <arg2> ...
 # may need -v option to mount data file/folder if they are used as arguments.
 docker run -v /data1/:/d1/:rw -v /data2/:/d2/:rw 4dndcic/4dn-bedtobeddb <run-xx.sh> /d1/file1 /d2/file2 ...
 ```
+
+### run-bedtobeddb.sh
+This converts a bed file format into beddb to be visualized in Higlass
+* Input: a bed file
+* Output: a beddb file
+
+#### Usage
+Run the following in the container
+```
+run-bedtobeddb <bedfile> <assembly> <outdir>
+# bedfile: input bedfile
+# assembly: the genome assembly
+# outdir: output directory
+```