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db_dump.sql
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db_dump.sql
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--
-- PostgreSQL database dump
--
SET statement_timeout = 0;
SET lock_timeout = 0;
SET client_encoding = 'UTF8';
SET standard_conforming_strings = on;
SET check_function_bodies = false;
SET client_min_messages = warning;
--
-- Name: plpgsql; Type: EXTENSION; Schema: -; Owner:
--
CREATE EXTENSION IF NOT EXISTS plpgsql WITH SCHEMA pg_catalog;
--
-- Name: EXTENSION plpgsql; Type: COMMENT; Schema: -; Owner:
--
COMMENT ON EXTENSION plpgsql IS 'PL/pgSQL procedural language';
SET search_path = public, pg_catalog;
--
-- Name: container_id_seq; Type: SEQUENCE; Schema: public; Owner: dockstore
--
CREATE SEQUENCE container_id_seq
START WITH 1
INCREMENT BY 50
NO MINVALUE
NO MAXVALUE
CACHE 1;
ALTER TABLE public.container_id_seq OWNER TO postgres;
SET default_tablespace = '';
SET default_with_oids = false;
--
-- Name: enduser; Type: TABLE; Schema: public; Owner: dockstore; Tablespace:
--
CREATE TABLE enduser (
id bigint NOT NULL,
isadmin boolean,
username character varying(255) NOT NULL
);
ALTER TABLE public.enduser OWNER TO postgres;
--
-- Name: enduser_id_seq; Type: SEQUENCE; Schema: public; Owner: dockstore
--
CREATE SEQUENCE enduser_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
NO MAXVALUE
CACHE 1;
ALTER TABLE public.enduser_id_seq OWNER TO postgres;
--
-- Name: enduser_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: dockstore
--
ALTER SEQUENCE enduser_id_seq OWNED BY enduser.id;
--
-- Name: endusergroup; Type: TABLE; Schema: public; Owner: dockstore; Tablespace:
--
CREATE TABLE endusergroup (
groupid bigint NOT NULL,
userid bigint NOT NULL
);
ALTER TABLE public.endusergroup OWNER TO postgres;
--
-- Name: entry_label; Type: TABLE; Schema: public; Owner: dockstore; Tablespace:
--
CREATE TABLE entry_label (
entryid bigint NOT NULL,
labelid bigint NOT NULL
);
ALTER TABLE public.entry_label OWNER TO postgres;
--
-- Name: label; Type: TABLE; Schema: public; Owner: dockstore; Tablespace:
--
CREATE TABLE label (
id bigint NOT NULL,
value character varying(255)
);
ALTER TABLE public.label OWNER TO postgres;
--
-- Name: label_id_seq; Type: SEQUENCE; Schema: public; Owner: dockstore
--
CREATE SEQUENCE label_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
NO MAXVALUE
CACHE 1;
ALTER TABLE public.label_id_seq OWNER TO postgres;
--
-- Name: label_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: dockstore
--
ALTER SEQUENCE label_id_seq OWNED BY label.id;
--
-- Name: sourcefile; Type: TABLE; Schema: public; Owner: dockstore; Tablespace:
--
CREATE TABLE sourcefile (
id bigint NOT NULL,
content text,
path character varying(255) NOT NULL,
type character varying(255)
);
ALTER TABLE public.sourcefile OWNER TO postgres;
--
-- Name: sourcefile_id_seq; Type: SEQUENCE; Schema: public; Owner: dockstore
--
CREATE SEQUENCE sourcefile_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
NO MAXVALUE
CACHE 1;
ALTER TABLE public.sourcefile_id_seq OWNER TO postgres;
--
-- Name: sourcefile_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: dockstore
--
ALTER SEQUENCE sourcefile_id_seq OWNED BY sourcefile.id;
--
-- Name: tag; Type: TABLE; Schema: public; Owner: dockstore; Tablespace:
--
CREATE TABLE tag (
id bigint NOT NULL,
dirtybit boolean,
hidden boolean,
lastmodified timestamp without time zone,
name character varying(255),
reference character varying(255),
valid boolean,
verified boolean,
verifiedsource character varying(255),
automated boolean,
cwlpath text NOT NULL,
dockerfilepath text NOT NULL,
imageid character varying(255),
size bigint,
wdlpath text NOT NULL
);
ALTER TABLE public.tag OWNER TO postgres;
--
-- Name: tag_id_seq; Type: SEQUENCE; Schema: public; Owner: dockstore
--
CREATE SEQUENCE tag_id_seq
START WITH 1
INCREMENT BY 50
NO MINVALUE
NO MAXVALUE
CACHE 1;
ALTER TABLE public.tag_id_seq OWNER TO postgres;
--
-- Name: token; Type: TABLE; Schema: public; Owner: dockstore; Tablespace:
--
CREATE TABLE token (
id bigint NOT NULL,
content character varying(255) NOT NULL,
refreshtoken character varying(255),
tokensource character varying(255) NOT NULL,
userid bigint,
username character varying(255) NOT NULL
);
ALTER TABLE public.token OWNER TO postgres;
--
-- Name: token_id_seq; Type: SEQUENCE; Schema: public; Owner: dockstore
--
CREATE SEQUENCE token_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
NO MAXVALUE
CACHE 1;
ALTER TABLE public.token_id_seq OWNER TO postgres;
--
-- Name: token_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: dockstore
--
ALTER SEQUENCE token_id_seq OWNED BY token.id;
--
-- Name: tool; Type: TABLE; Schema: public; Owner: dockstore; Tablespace:
--
CREATE TABLE tool (
id bigint NOT NULL,
author character varying(255),
defaultversion character varying(255),
description text,
email character varying(255),
giturl character varying(255),
ispublished boolean,
lastmodified integer,
lastupdated timestamp without time zone,
defaultcwlpath text,
defaultdockerfilepath text,
defaultwdlpath text,
lastbuild timestamp without time zone,
mode text DEFAULT 'AUTO_DETECT_QUAY_TAGS_AUTOMATED_BUILDS'::text NOT NULL,
name character varying(255) NOT NULL,
namespace character varying(255),
path character varying(255),
registry character varying(255) NOT NULL,
toolname character varying(255) NOT NULL,
toolmaintaineremail character varying(255),
privateaccess boolean
);
ALTER TABLE public.tool OWNER TO postgres;
--
-- Name: tool_tag; Type: TABLE; Schema: public; Owner: dockstore; Tablespace:
--
CREATE TABLE tool_tag (
toolid bigint NOT NULL,
tagid bigint NOT NULL
);
ALTER TABLE public.tool_tag OWNER TO postgres;
--
-- Name: user_entry; Type: TABLE; Schema: public; Owner: dockstore; Tablespace:
--
CREATE TABLE user_entry (
userid bigint NOT NULL,
entryid bigint NOT NULL
);
ALTER TABLE public.user_entry OWNER TO postgres;
--
-- Name: usergroup; Type: TABLE; Schema: public; Owner: dockstore; Tablespace:
--
CREATE TABLE usergroup (
id bigint NOT NULL,
name character varying(255) NOT NULL
);
ALTER TABLE public.usergroup OWNER TO postgres;
--
-- Name: usergroup_id_seq; Type: SEQUENCE; Schema: public; Owner: dockstore
--
CREATE SEQUENCE usergroup_id_seq
START WITH 1
INCREMENT BY 1
NO MINVALUE
NO MAXVALUE
CACHE 1;
ALTER TABLE public.usergroup_id_seq OWNER TO postgres;
--
-- Name: usergroup_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: dockstore
--
ALTER SEQUENCE usergroup_id_seq OWNED BY usergroup.id;
--
-- Name: version_sourcefile; Type: TABLE; Schema: public; Owner: dockstore; Tablespace:
--
CREATE TABLE version_sourcefile (
versionid bigint NOT NULL,
sourcefileid bigint NOT NULL
);
ALTER TABLE public.version_sourcefile OWNER TO postgres;
--
-- Name: workflow; Type: TABLE; Schema: public; Owner: dockstore; Tablespace:
--
CREATE TABLE workflow (
id bigint NOT NULL,
author character varying(255),
defaultversion character varying(255),
description text,
email character varying(255),
giturl character varying(255),
ispublished boolean,
lastmodified integer,
lastupdated timestamp without time zone,
defaultworkflowpath text,
descriptortype character varying(255) NOT NULL,
mode text DEFAULT 'STUB'::text NOT NULL,
organization character varying(255) NOT NULL,
path character varying(255),
repository character varying(255) NOT NULL,
workflowname text
);
ALTER TABLE public.workflow OWNER TO postgres;
--
-- Name: workflow_workflowversion; Type: TABLE; Schema: public; Owner: dockstore; Tablespace:
--
CREATE TABLE workflow_workflowversion (
workflowid bigint NOT NULL,
workflowversionid bigint NOT NULL
);
ALTER TABLE public.workflow_workflowversion OWNER TO postgres;
--
-- Name: workflowversion; Type: TABLE; Schema: public; Owner: dockstore; Tablespace:
--
CREATE TABLE workflowversion (
id bigint NOT NULL,
dirtybit boolean,
hidden boolean,
lastmodified timestamp without time zone,
name character varying(255),
reference character varying(255),
valid boolean,
verified boolean,
verifiedsource character varying(255),
workflowpath text NOT NULL
);
ALTER TABLE public.workflowversion OWNER TO postgres;
--
-- Name: id; Type: DEFAULT; Schema: public; Owner: dockstore
--
ALTER TABLE ONLY enduser ALTER COLUMN id SET DEFAULT nextval('enduser_id_seq'::regclass);
--
-- Name: id; Type: DEFAULT; Schema: public; Owner: dockstore
--
ALTER TABLE ONLY label ALTER COLUMN id SET DEFAULT nextval('label_id_seq'::regclass);
--
-- Name: id; Type: DEFAULT; Schema: public; Owner: dockstore
--
ALTER TABLE ONLY sourcefile ALTER COLUMN id SET DEFAULT nextval('sourcefile_id_seq'::regclass);
--
-- Name: id; Type: DEFAULT; Schema: public; Owner: dockstore
--
ALTER TABLE ONLY token ALTER COLUMN id SET DEFAULT nextval('token_id_seq'::regclass);
--
-- Name: id; Type: DEFAULT; Schema: public; Owner: dockstore
--
ALTER TABLE ONLY usergroup ALTER COLUMN id SET DEFAULT nextval('usergroup_id_seq'::regclass);
--
-- Name: container_id_seq; Type: SEQUENCE SET; Schema: public; Owner: dockstore
--
SELECT pg_catalog.setval('container_id_seq', 51, true);
--
-- Data for Name: enduser; Type: TABLE DATA; Schema: public; Owner: dockstore
--
INSERT INTO enduser VALUES (1, false, 'user_A');
--
-- Name: enduser_id_seq; Type: SEQUENCE SET; Schema: public; Owner: dockstore
--
SELECT pg_catalog.setval('enduser_id_seq', 1, true);
--
-- Data for Name: endusergroup; Type: TABLE DATA; Schema: public; Owner: dockstore
--
--
-- Data for Name: entry_label; Type: TABLE DATA; Schema: public; Owner: dockstore
--
--
-- Data for Name: label; Type: TABLE DATA; Schema: public; Owner: dockstore
--
--
-- Name: label_id_seq; Type: SEQUENCE SET; Schema: public; Owner: dockstore
--
SELECT pg_catalog.setval('label_id_seq', 1, false);
--
-- Data for Name: sourcefile; Type: TABLE DATA; Schema: public; Owner: dockstore
--
INSERT INTO sourcefile VALUES (1, 'cwlVersion: v1.0 class: CommandLineTool baseCommand: echo inputs: message: type: string inputBinding: position: 1 outputs: []', '/Dockstore.cwl', 'DOCKSTORE_CWL');
INSERT INTO sourcefile VALUES (2, 'FROM docker/whalesay:latest
RUN apt-get -y update && apt-get install -y fortunes
CMD /usr/games/fortune -a | cowsay
', '/Dockerfile', 'DOCKERFILE');
INSERT INTO sourcefile VALUES (3, 'cwlVersion: v1.0 class: CommandLineTool baseCommand: echo inputs: message: type: string inputBinding: position: 1 outputs: []', '/Dockstore.cwl', 'DOCKSTORE_CWL');
INSERT INTO sourcefile VALUES (4, 'task hello {
String name
command {
echo ''hello ${name}!''
}
output {
File response = stdout()
}
}
workflow test {
call hello
}
', '/Dockstore.wdl', 'DOCKSTORE_WDL');
INSERT INTO sourcefile VALUES (5, 'FROM docker/whalesay:latest
RUN apt-get -y update && apt-get install -y fortunes
CMD /usr/games/fortune -a | cowsay
', '/Dockerfile', 'DOCKERFILE');
INSERT INTO sourcefile VALUES (6, 'cwlVersion: v1.0 class: CommandLineTool baseCommand: echo inputs: message: type: string inputBinding: position: 1 outputs: []', '/Dockstore.cwl', 'DOCKSTORE_CWL');
INSERT INTO sourcefile VALUES (7, 'task hello {
String name
command {
echo ''hello ${name}!''
}
output {
File response = stdout()
}
}
workflow test {
call hello
}
', '/Dockstore.wdl', 'DOCKSTORE_WDL');
INSERT INTO sourcefile VALUES (8, 'FROM docker/whalesay:latest
RUN apt-get -y update && apt-get install -y fortunes
CMD /usr/games/fortune -a | cowsay
', '/Dockerfile', 'DOCKERFILE');
INSERT INTO sourcefile VALUES (9, 'cwlVersion: v1.0 class: CommandLineTool baseCommand: echo inputs: message: type: string inputBinding: position: 1 outputs: []', '/Dockstore.cwl', 'DOCKSTORE_CWL');
INSERT INTO sourcefile VALUES (10, 'FROM docker/whalesay:latest
RUN apt-get -y update && apt-get install -y fortunes
CMD /usr/games/fortune -a | cowsay
', '/Dockerfile', 'DOCKERFILE');
INSERT INTO sourcefile VALUES (11, 'cwlVersion: v1.0 class: CommandLineTool baseCommand: echo inputs: message: type: string inputBinding: position: 1 outputs: []', '/Dockstore.cwl', 'DOCKSTORE_CWL');
INSERT INTO sourcefile VALUES (12, 'FROM docker/whalesay:latest
RUN apt-get -y update && apt-get install -y fortunes
CMD /usr/games/fortune -a | cowsay
', '/Dockerfile', 'DOCKERFILE');
INSERT INTO sourcefile VALUES (13, 'task hello {
String name
command {
echo ''hello ${name}!''
}
output {
File response = stdout()
}
}
workflow test {
call hello
}
', '/Dockstore.wdl', 'DOCKSTORE_WDL');
INSERT INTO sourcefile VALUES (14, 'FROM docker/whalesay:latest
RUN apt-get -y update && apt-get install -y fortunes
CMD /usr/games/fortune -a | cowsay
', '/Dockerfile', 'DOCKERFILE');
INSERT INTO sourcefile VALUES (15, 'task hello {
String name
command {
echo ''hello ${name}!''
}
output {
File response = stdout()
}
}
workflow test {
call hello
}
', '/Dockstore.wdl', 'DOCKSTORE_WDL');
INSERT INTO sourcefile VALUES (16, 'FROM docker/whalesay:latest
RUN apt-get -y update && apt-get install -y fortunes
CMD /usr/games/fortune -a | cowsay
', '/Dockerfile', 'DOCKERFILE');
INSERT INTO sourcefile VALUES (17, 'class: s:SoftwareSourceCode
s:name: "alea"
s:about: >
ALEA is a computational toolbox for allele-specific (AS) epigenomics analysis, which incorporates allelic variation data within existing
resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants
in human and mouse cells. ALEA provides a customizable pipeline of command line tools for AS analysis of next-generation sequencing data
(ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers.
ALEA takes advantage of the available genomic resources for human (The 1000 Genomes Project Consortium) and mouse (The Mouse Genome Project)
to reconstruct diploid in silico genomes for human samples or hybrid mouse samples under study. Then, for each accompanying ChIP-seq or
RNA-seq dataset, ALEA generates two wig files from short reads aligned differentially to each haplotype.
This pipeline has been validated using human and hybrid mouse ChIP-seq and RNA-seq data (See Test Data section).
s:targetProduct:
class: s:SoftwareApplication
s:downloadUrl: ftp://ftp.bcgsc.ca/supplementary/ALEA/files/alea.1.2.2.tar.gz
s:softwareVersion: "1.2.2"
s:applicationCategory: "command line tool"
s:url: http://www.bcgsc.ca/platform/bioinfo/software/alea
s:license: https://opensource.org/licenses/AFL-3.0
s:programmingLanguage: "JAVA"
s:publication:
- id: http://dx.doi.org/10.1093/bioinformatics/btt744
s:author:
- class: s:Person
id: mailto:mkarimi@bcgsc.ca
s:name: "Mohammad Karimi"
s:email: mailto:mkarimi@bcgsc.ca
s:url: http://www.bcgsc.ca/author/mkarimi
s:worksFor:
- class: s:Organization
s:name: "Canada''s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada"
- class: s:Organization
s:name: "Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada"
', 'alea-metadata.yaml', 'DOCKSTORE_CWL');
INSERT INTO sourcefile VALUES (18, 'class: EnvVarRequirement
envDef:
- envName: "PATH"
envValue: "/usr/local/bin/:/usr/bin:/bin"
', 'envvar-global.yml', 'DOCKSTORE_CWL');
INSERT INTO sourcefile VALUES (19, 'class: DockerRequirement
dockerPull: scidap/alea:v1.2.2
#dockerImageId: scidap/alea:v1.2.2 #not yet ready
dockerFile: |
#################################################################
# Dockerfile
#
# Software: Alea
# Software Version: 1.2.2
# Description: Alea image for SciDAP
# Website: http://scidap.com/
# Provides: alea|bwa|Plink|vcftools|bedGraphToBigWig|shapeit2
# Base Image: scidap/scidap:v0.0.1
# Build Cmd: docker build --rm -t scidap/alea:v1.2.2 .
# Pull Cmd: docker pull scidap/alea:v1.2.2
# Run Cmd: docker run --rm scidap/alea:v1.2.2 alea
#################################################################
### Base Image
FROM scidap/scidap:v0.0.1
MAINTAINER Andrey V Kartashov "porter@porter.st"
ENV DEBIAN_FRONTEND noninteractive
################## BEGIN INSTALLATION ######################
WORKDIR /tmp
### Install required packages (samtools)
RUN apt-get clean all &&\
apt-get update &&\
apt-get install -y \
libncurses5-dev && \
apt-get clean && \
apt-get purge && \
rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /usr/share/doc/*
### Installing BWA
ENV VERSION 0.7.12
ENV NAME bwa
ENV URL "https://github.com/lh3/bwa/archive/${VERSION}.tar.gz"
RUN wget -q -O - $URL | tar -zxv && \
cd ${NAME}-${VERSION} && \
make -j 4 && \
cd .. && \
cp ./${NAME}-${VERSION}/${NAME} /usr/local/bin/ && \
strip /usr/local/bin/${NAME}; true && \
rm -rf ./${NAME}-${VERSION}/
# ### Installing bowtie
#
# ENV VERSION 1.1.2
# ENV NAME bowtie
# ENV URL "https://github.com/BenLangmead/bowtie/archive/v${VERSION}.tar.gz"
#
# RUN wget -q -O - $URL | tar -zxv && \
# cd ${NAME}-${VERSION} && \
# make -j 4 && \
# cd .. && \
# cp ./${NAME}-${VERSION}/${NAME} /usr/local/bin/ && \
# cp ./${NAME}-${VERSION}/${NAME}-* /usr/local/bin/ && \
# strip /usr/local/bin/*; true && \
# rm -rf ./${NAME}-${VERSION}/
### Installing samtools/htslib/tabix/bgzip
ENV VERSIONH 1.2.1
ENV NAMEH htslib
ENV URLH "https://github.com/samtools/htslib/archive/${VERSIONH}.tar.gz"
ENV VERSION "1.2"
ENV NAME "samtools"
ENV URL "https://github.com/samtools/samtools/archive/${VERSION}.tar.gz"
RUN wget -q -O - $URLH | tar -zxv && \
cd ${NAMEH}-${VERSIONH} && \
make -j 4 && \
cd .. && \
cp ./${NAMEH}-${VERSIONH}/tabix /usr/local/bin/ && \
cp ./${NAMEH}-${VERSIONH}/bgzip /usr/local/bin/ && \
cp ./${NAMEH}-${VERSIONH}/htsfile /usr/local/bin/ && \
strip /usr/local/bin/tabix; true && \
strip /usr/local/bin/bgzip; true && \
strip /usr/local/bin/htsfile; true && \
ln -s ./${NAMEH}-${VERSIONH}/ ./${NAMEH} && \
wget -q -O - $URL | tar -zxv && \
cd ${NAME}-${VERSION} && \
make -j 4 && \
cd .. && \
cp ./${NAME}-${VERSION}/${NAME} /usr/local/bin/ && \
strip /usr/local/bin/${NAME}; true && \
rm -rf ./${NAMEH}-${VERSIONH}/ && \
rm -rf ./${NAME}-${VERSION}/
### Installing bedGraphToBigWig
RUN wget -q -O /usr/local/bin/bedGraphToBigWig http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig && \
chmod a+x /usr/local/bin/bedGraphToBigWig
### Installing VCFTools
ENV VERSION 0.1.14
ENV NAME vcftools
ENV URL "https://github.com/vcftools/vcftools/releases/download/v${VERSION}/${NAME}-${VERSION}.tar.gz"
RUN wget -q -O - $URL | tar -zxv && \
cd ${NAME}-${VERSION} && \
./configure --prefix=/usr/local && \
make -j 4 install && \
cd .. && \
rm -rf ./${NAME}-${VERSION}/
### Installing SHAPEIT2
RUN wget -q -O - https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.v2.r837.GLIBCv2.20.Linux.static.tgz|tar -zxv -C /usr/local bin/shapeit && \
chmod a+x /usr/local/bin/shapeit
### Installing plink
RUN wget -q -O plink-1.07-x86_64.zip http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-1.07-x86_64.zip && \
unzip plink-1.07-x86_64.zip && \
cp plink-1.07-x86_64/* /usr/local/bin && \
rm -rf plink-1.07-x86_64 && \
rm -f plink-1.07-x86_64.zip
### Installing alea
RUN wget -q -O - ftp://ftp.bcgsc.ca/supplementary/ALEA/files/alea.1.2.2.tar.gz | tar -zxv -C /usr/local --strip-components=1 && \
cd /usr/local/bin/ && \
printf ''144c144\n< --output-fasta="$VAR_GENOME1_SNPS"\n---\n> --output-fasta="$VAR_GENOME2_SNPS"\n''| patch createGenome.sh && \
sed -i.bak s/^AL_BWA_ALN_PARAMS/#AL_BWA_ALN_PARAMS/g alea.config && \
sed -i.bak s/^AL_USE_CONCATENATED_GENOME/#AL_USE_CONCATENATED_GENOME/g alea.config && \
rm -f alea.config.bak
', 'alea-docker.yml', 'DOCKSTORE_CWL');
INSERT INTO sourcefile VALUES (28, 'cwlVersion: v1.0
class: Workflow
inputs:
inp: File
ex: string
outputs:
classout:
type: File
outputSource: compile/classfile
steps:
untar:
run: tar-param.cwl
in:
tarfile: inp
extractfile: ex
out: [example_out]
compile:
run: arguments.cwl
in:
src: untar/example_out
out: [classfile]
wrkflow:
run: grep-and-count.cwl
in:
infiles: inp
pattern: "hello"
out: [outfile]
', '/1st-workflow.cwl', 'DOCKSTORE_CWL');
INSERT INTO sourcefile VALUES (29, '#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.0
inputs:
pattern:
type: string
inputBinding: {position: 0}
infile:
type: File
inputBinding: {position: 1}
outputs:
outfile:
type: stdout
baseCommand: grep
', 'grep.cwl', 'DOCKSTORE_CWL');
INSERT INTO sourcefile VALUES (30, '#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.0
inputs:
infiles:
type: File[]
inputBinding: {position: 1}
outputs:
outfile:
type: stdout
baseCommand: [wc, -l]
', 'wc.cwl', 'DOCKSTORE_CWL');
INSERT INTO sourcefile VALUES (20, '#!/usr/bin/env cwl-runner
cwlVersion: "cwl:draft-3"
class: CommandLineTool
requirements:
- $import: envvar-global.yml
- $import: alea-docker.yml
- class: InlineJavascriptRequirement
inputs:
- id: "#hapsDir"
type: File
description: |
path to the directory containing the .haps files
inputBinding:
position: 2
- id: "#unphased"
type: File
description: |
path to the vcf file containing unphased SNPs and Indels
inputBinding:
position: 3
- id: "#outputPrefix"
type: string
description: |
output file prefix including the path but not the extension
inputBinding:
position: 3
outputs:
- id: "#phasevcf"
type: File
description: "Creates the file outputPrefix.vcf.gz"
outputBinding:
glob: $(inputs.outputPrefix+".vcf.gz")
baseCommand: ["alea", "phaseVCF"]
$namespaces:
s: http://schema.org/
$schemas:
- https://sparql-test.commonwl.org/schema.rdf
s:mainEntity:
$import: alea-metadata.yaml
s:downloadUrl: https://github.com/common-workflow-language/workflows/blob/master/tools/alea-phaseVCF.cwl
s:codeRepository: https://github.com/common-workflow-language/workflows
s:license: http://www.apache.org/licenses/LICENSE-2.0
s:isPartOf:
class: s:CreativeWork
s:name: "Common Workflow Language"
s:url: http://commonwl.org/
s:author:
class: s:Person
s:name: "Andrey Kartashov"
s:email: mailto:Andrey.Kartashov@cchmc.org
s:sameAs:
- id: http://orcid.org/0000-0001-9102-5681
s:worksFor:
- class: s:Organization
s:name: "Cincinnati Children''s Hospital Medical Center"
s:location: "3333 Burnet Ave, Cincinnati, OH 45229-3026"
s:department:
- class: s:Organization
s:name: "Barski Lab"
', '/Dockstore.cwl', 'DOCKSTORE_CWL');
INSERT INTO sourcefile VALUES (21, 'FROM ubuntu:12.04
', '/Dockerfile', 'DOCKERFILE');
INSERT INTO sourcefile VALUES (22, 'class: s:SoftwareSourceCode
s:name: "alea"
s:about: >
ALEA is a computational toolbox for allele-specific (AS) epigenomics analysis, which incorporates allelic variation data within existing
resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants
in human and mouse cells. ALEA provides a customizable pipeline of command line tools for AS analysis of next-generation sequencing data
(ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers.
ALEA takes advantage of the available genomic resources for human (The 1000 Genomes Project Consortium) and mouse (The Mouse Genome Project)
to reconstruct diploid in silico genomes for human samples or hybrid mouse samples under study. Then, for each accompanying ChIP-seq or
RNA-seq dataset, ALEA generates two wig files from short reads aligned differentially to each haplotype.
This pipeline has been validated using human and hybrid mouse ChIP-seq and RNA-seq data (See Test Data section).
s:targetProduct:
class: s:SoftwareApplication
s:downloadUrl: ftp://ftp.bcgsc.ca/supplementary/ALEA/files/alea.1.2.2.tar.gz
s:softwareVersion: "1.2.2"
s:applicationCategory: "command line tool"
s:url: http://www.bcgsc.ca/platform/bioinfo/software/alea
s:license: https://opensource.org/licenses/AFL-3.0
s:programmingLanguage: "JAVA"
s:publication:
- id: http://dx.doi.org/10.1093/bioinformatics/btt744
s:author:
- class: s:Person
id: mailto:mkarimi@bcgsc.ca
s:name: "Mohammad Karimi"
s:email: mailto:mkarimi@bcgsc.ca
s:url: http://www.bcgsc.ca/author/mkarimi
s:worksFor:
- class: s:Organization
s:name: "Canada''s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada"
- class: s:Organization
s:name: "Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada"
', 'alea-metadata.yaml', 'DOCKSTORE_CWL');
INSERT INTO sourcefile VALUES (23, 'class: EnvVarRequirement
envDef:
- envName: "PATH"
envValue: "/usr/local/bin/:/usr/bin:/bin"
', 'envvar-global.yml', 'DOCKSTORE_CWL');
INSERT INTO sourcefile VALUES (24, 'class: DockerRequirement
dockerPull: scidap/alea:v1.2.2
#dockerImageId: scidap/alea:v1.2.2 #not yet ready
dockerFile: |
#################################################################
# Dockerfile
#
# Software: Alea
# Software Version: 1.2.2
# Description: Alea image for SciDAP
# Website: http://scidap.com/
# Provides: alea|bwa|Plink|vcftools|bedGraphToBigWig|shapeit2
# Base Image: scidap/scidap:v0.0.1
# Build Cmd: docker build --rm -t scidap/alea:v1.2.2 .
# Pull Cmd: docker pull scidap/alea:v1.2.2
# Run Cmd: docker run --rm scidap/alea:v1.2.2 alea
#################################################################
### Base Image
FROM scidap/scidap:v0.0.1
MAINTAINER Andrey V Kartashov "porter@porter.st"
ENV DEBIAN_FRONTEND noninteractive
################## BEGIN INSTALLATION ######################
WORKDIR /tmp
### Install required packages (samtools)
RUN apt-get clean all &&\
apt-get update &&\
apt-get install -y \
libncurses5-dev && \