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V2 #1

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16 changes: 15 additions & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
```
4 changes: 1 addition & 3 deletions scripts/run-bedtobeddb.sh
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand All @@ -20,7 +19,6 @@ fi
gunzip -c $INPUT > pp.bed

outputfile="$OUTDIR/$FILE_NAME.beddb"
echo $outputfile

clodius aggregate bedfile \
--assembly $ASSEMBLY -o $outputfile \
Expand Down