diff --git a/.travis.yml b/.travis.yml index c64ffb4..c37d550 100644 --- a/.travis.yml +++ b/.travis.yml @@ -2,10 +2,6 @@ sudo: required language: c python python: 3.6 os: linux -addons: - apt: - packages: - - oracle-java8-installer services: - docker diff --git a/Dockerfile b/Dockerfile index 2735c9f..50301ee 100644 --- a/Dockerfile +++ b/Dockerfile @@ -26,10 +26,22 @@ RUN apt-get update -y && apt-get install -y \ vim \ wget \ zlib1g-dev \ - libmysqlclient-dev - + libmysqlclient-dev \ + libsqlite3-dev + +# install python 3.6 +RUN wget https://www.python.org/ftp/python/3.6.0/Python-3.6.0.tar.xz +RUN tar xvf Python-3.6.0.tar.xz +WORKDIR Python-3.6.0 +RUN ./configure +RUN make +RUN make altinstall + + # installing python libraries -RUN pip install scipy==1.1.0 +RUN pip3.6 install --upgrade pip +RUN pip3.6 install cython==0.29.21 + # download tools WORKDIR /usr/local/bin @@ -38,7 +50,7 @@ RUN . downloads.sh # set path ENV PATH=/usr/local/bin/scripts:$PATH - + # supporting UTF-8 ENV LC_ALL=C.UTF-8 ENV LANG=C.UTF-8 diff --git a/README.md b/README.md index 47f1e3f..5522070 100644 --- a/README.md +++ b/README.md @@ -60,3 +60,17 @@ docker run 4dndcic/4dn-bedtobeddb ... # 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 /d1/file1 /d2/file2 ... ``` + +### run-bedtobeddb.sh +This takes a bed file and a chromsizes files and converts it to beddb to be compatible with higlass visualization. +* Input: a bed file and a chromsizes file +* Output: a beddb file + +#### Usage +Runs the following in the container +``` +run-bedtibeddb.sh +# bedfile: input bed +# chromsizes: chromsizes file +# outdir: output directory +``` diff --git a/bed2beddb_v3_insert_workflow.json b/bed2beddb_v3_insert_workflow.json new file mode 100755 index 0000000..9232d5e --- /dev/null +++ b/bed2beddb_v3_insert_workflow.json @@ -0,0 +1,97 @@ +{ + "app_name": "bedtobeddb", + "app_version": "v3", + "arguments": [ + { + "argument_format": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", + "argument_type": "Input file", + "workflow_argument_name": "bedfile" + }, + { + "argument_format": "d13d06cf-218e-4f61-55f0-93f226248b2c", + "argument_type": "Input file", + "workflow_argument_name": "chromsizes_file" + }, + { + "argument_format": "76dc8c06-67d8-487b-8fc8-d841752a0b60", + "argument_type": "Output to-be-extra-input file", + "extra_file_use_for": "visualization", + "workflow_argument_name": "beddbfile", + "argument_to_be_attached_to": "bedfile" + } + ], + + "award": "1U01CA200059-01", + "category": ["format conversion"], + "cwl_child_filenames": [], + "cwl_directory_url": "https://raw.githubusercontent.com/4dn-dcic/docker-4dn-bedtobeddb/v3/cwl/", + "cwl_main_filename": "bedtobeddb.cwl", + "cwl_pointer": "", + "version_upgrade_log": "Uses chromsizes files instead of the assembly parameter", + "description": "Converting bed to beddb", + "docker_image_name": "4dn-dcic/docker-4dn-bedtobeddb", + "docker_registry_url": "https://hub.docker.com/", + "lab": "4dn-dcic-lab", + "name": "bedtobeddb", + "steps": [ + { + "inputs": [ + { + "meta": { + "cardinality": "single", + "file_format": "69f6d609-f2ac-4c82-9472-1a13331b5ce9", + "global": true, + "type": "data file" + }, + "name": "bedfile", + "source": [ + { + "name": "bedfile" + } + ] + }, + { + "meta": { + "cardinality": "single", + "file_format": "d13d06cf-218e-4f61-55f0-93f226248b2c", + "global": true, + "type": "data file" + }, + "name": "chromsizes_file", + "source": [ + { + "name": "chromsizes_file" + } + ] + } + ], + "meta": { + "analysis_step_types": [ + "file format conversion" + ], + "software_used": [ + "/softwares/ac810b99-9d59-4435-8829-477aedf4ca54/" + ] + }, + "name": "bedtobeddb", + "outputs": [ + { + "meta": { + "cardinality": "single", + "file_format": "76dc8c06-67d8-487b-8fc8-d841752a0b60", + "global": true, + "type": "data file" + }, + "name": "beddbfile", + "target": [ + { + "name": "beddbfile" + } + ] + } + ] + } + ], + "title": "Converting bed to beddb v3", + "uuid": "91049eef-d434-4e16-a1ad-06de73f079dc" + } diff --git a/cwl/bedtobeddb.cwl b/cwl/bedtobeddb.cwl index 30d3f3f..c5693fb 100644 --- a/cwl/bedtobeddb.cwl +++ b/cwl/bedtobeddb.cwl @@ -6,7 +6,7 @@ cwlVersion: v1.0 requirements: - class: DockerRequirement - dockerPull: "4dndcic/4dn-bedtobeddb:v2" + dockerPull: "4dndcic/4dn-bedtobeddb:v3" - class: "InlineJavascriptRequirement" @@ -16,8 +16,8 @@ inputs: inputBinding: position: 1 - assembly: - type: string + chromsizes_file: + type: File inputBinding: position: 2 diff --git a/downloads.sh b/downloads.sh index 919140f..fc62074 100644 --- a/downloads.sh +++ b/downloads.sh @@ -1,7 +1,5 @@ ## SOFTWARE: clodius -## VERSION: 0.9.4 +## VERSION: 0.15.1 ## TYPE: Tile generator for big data ## SOURCE URL: https://github.com/higlass/clodius -pip install clodius==0.9.4 - - +pip3.6 install clodius==0.15.1 diff --git a/scripts/run-bedtobeddb.sh b/scripts/run-bedtobeddb.sh index 8a97610..fe02b57 100644 --- a/scripts/run-bedtobeddb.sh +++ b/scripts/run-bedtobeddb.sh @@ -3,12 +3,11 @@ # Aggregates a Bed file to a format compatible with higlass (beddb) INPUT=$1 -ASSEMBLY=$2 +CHROMSIZES=$2 OUTDIR=$3 FILE_BASE=$(basename $INPUT) -FILE_NAME=${FILE_BASE%.*} -echo $FILE_NAME +FILE_NAME=${FILE_BASE%%.*} mkfifo pp @@ -20,10 +19,9 @@ fi gunzip -c $INPUT > pp.bed outputfile="$OUTDIR/$FILE_NAME.beddb" -echo $outputfile clodius aggregate bedfile \ - --assembly $ASSEMBLY -o $outputfile \ + --chromsizes-filename $CHROMSIZES -o $outputfile \ pp.bed rm pp diff --git a/test_data/Boundaries_genomewideES8kbhg38merge_adjust2_PCA_0.25v2_2.bed b/test_data/Boundaries_genomewideES8kbhg38merge_adjust2_PCA_0.25v2_2.bed new file mode 100644 index 0000000..d35b0f9 --- /dev/null +++ b/test_data/Boundaries_genomewideES8kbhg38merge_adjust2_PCA_0.25v2_2.bed @@ -0,0 +1,10811 @@ +chrX 2640000 2640001 +chrX 2864000 2864001 +chrX 3824000 3824001 +chrX 3632000 3632001 +chrX 3064000 3064001 +chrX 3560000 3560001 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144432000 +chr8 143944000 144336000 \ No newline at end of file diff --git a/test_data/Communities_genomewideES8kbhg38merge_adjust2_PCA_0.25v2_2.bed.beddb b/test_data/Communities_genomewideES8kbhg38merge_adjust2_PCA_0.25v2_2.bed.beddb new file mode 100644 index 0000000..b0d6be6 Binary files /dev/null and b/test_data/Communities_genomewideES8kbhg38merge_adjust2_PCA_0.25v2_2.bed.beddb differ diff --git a/tests/test_files/4DNFI823LSII.chrom.sizes b/tests/test_files/4DNFI823LSII.chrom.sizes new file mode 100644 index 0000000..63962a6 --- /dev/null +++ b/tests/test_files/4DNFI823LSII.chrom.sizes @@ -0,0 +1,24 @@ +chr1 248956422 +chr2 242193529 +chr3 198295559 +chr4 190214555 +chr5 181538259 +chr6 170805979 +chr7 159345973 +chr8 145138636 +chr9 138394717 +chr10 133797422 +chr11 135086622 +chr12 133275309 +chr13 114364328 +chr14 107043718 +chr15 101991189 +chr16 90338345 +chr17 83257441 +chr18 80373285 +chr19 58617616 +chr20 64444167 +chr21 46709983 +chr22 50818468 +chrX 156040895 +chrY 57227415 diff --git a/tests/test_input_json/bedtobeddb.input.json b/tests/test_input_json/bedtobeddb.input.json index 880a79d..d44cdf3 100644 --- a/tests/test_input_json/bedtobeddb.input.json +++ b/tests/test_input_json/bedtobeddb.input.json @@ -3,5 +3,8 @@ "class": "File", "path": "../test_files/test_file1.bed.gz" }, - "assembly": "hg38" + "chromsizes_file": { + "class": "File", + "path": "../test_files/4DNFI823LSII.chrom.sizes" + } }