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73aa81e
Use config.groovy.template everywhere
Oct 14, 2016
06c5314
Don't use noverify by default
Oct 14, 2016
45b6c2a
Add java script to override default java
multimeric Oct 14, 2016
124bdd0
Merge branch 'dev' of github.com:MelbourneGenomics/cpipe into dev
multimeric Oct 14, 2016
b0e4b50
Export JAVA_OPTS to everything
Oct 14, 2016
11badea
Merge branch 'dev' of github.com:MelbourneGenomics/cpipe into dev
multimeric Oct 14, 2016
c111b53
Move java script to bin
multimeric Oct 14, 2016
5e463a6
Stop java infinite loop
Oct 14, 2016
10c0f0b
Fix java version checks
Oct 14, 2016
d779051
quoted java wrapper
Oct 17, 2016
1ae2766
Merge 2.3 changes
multimeric Oct 17, 2016
908dce4
Remove some Docker dependencies
multimeric Oct 18, 2016
7cf35b8
Put all dependencies into dockerfile, remove from tasks
multimeric Oct 18, 2016
10aff15
Remove docker dependencies from dodo.py
multimeric Oct 18, 2016
e7f67b4
Make cpipe script not always check java; allow delegation to bpipe co…
multimeric Oct 18, 2016
ed53b43
Document run command rather than pipeline
multimeric Oct 19, 2016
7480f80
Fox -noverify warning message
multimeric Oct 19, 2016
13d0906
don't override batch parameter with default
supernifty Oct 20, 2016
90d1a05
Use DATA instead of REFBASE
multimeric Oct 21, 2016
9bb855d
Docs initial commit
multimeric Oct 21, 2016
902cd41
Merge branch 'dev' of github.com:MelbourneGenomics/cpipe into dev
multimeric Oct 21, 2016
91e45cf
Fix table in configuration.md
multimeric Oct 21, 2016
5f29032
Added more internal links in docs
multimeric Oct 21, 2016
5c071aa
Merge branch 'dev' of github.com:MelbourneGenomics/cpipe into dev
multimeric Oct 21, 2016
cf3b821
Fix outputs.md table
multimeric Oct 21, 2016
b8e8a18
Fixes batches.md table again
multimeric Oct 21, 2016
34f6dfc
Bpipe config branch PR (#188)
multimeric Oct 22, 2016
6901c56
Basic rewrite of install process to use tools/install subdir
multimeric Oct 23, 2016
9686ee8
Fix copy_config tasks
multimeric Oct 24, 2016
a8cd08d
Rewrite download and compile tasks using shared functions
multimeric Oct 24, 2016
5235b51
More install rewriting
multimeric Oct 24, 2016
c8eaa97
Finished basic install rewrite
multimeric Oct 24, 2016
3ed5768
Finished rewrite; add various c libs to nectar
multimeric Oct 25, 2016
d6c1580
Installer fixes
multimeric Oct 25, 2016
c5fcc7b
Uploaded more assets
multimeric Oct 25, 2016
0691fc9
Installer fixes
multimeric Oct 25, 2016
0efcbe6
Update current.manifest properly
multimeric Oct 25, 2016
16e2ab2
Stop using c_libs
multimeric Oct 25, 2016
2ba4356
Fixed refence file nectar tasks
multimeric Oct 25, 2016
70e8d2a
More data asset fixes
multimeric Oct 25, 2016
8e618d2
Made to_temp download tasks
multimeric Oct 25, 2016
b3322f2
More Fixes
Oct 25, 2016
d542516
Fixed junit lib
multimeric Oct 25, 2016
d25f4f7
Move copy from temp files
multimeric Oct 25, 2016
b850105
Fixed chromosome sizes task
multimeric Oct 25, 2016
3a962a7
Set uptodate for all install tasks
multimeric Oct 25, 2016
a84d065
Merri fixes
Oct 25, 2016
f2bd17d
Merge branch 'install-rewrite' of https://github.com/MelbourneGenomic…
Oct 25, 2016
4c8c838
Fix copy_config tasks
multimeric Oct 24, 2016
ceb0c18
Fix fastqc install
multimeric Oct 26, 2016
73adf2b
Merge branch 'install-rewrite' of github.com:MelbourneGenomics/cpipe …
multimeric Oct 26, 2016
b4e4499
Remove current manifest forever
multimeric Oct 26, 2016
1fa5f2b
Fix junit
multimeric Oct 26, 2016
507cd20
Fixed ucsc nectar task
multimeric Oct 26, 2016
001f4c9
Fix for copying single files, fix overriding symlinks
multimeric Oct 26, 2016
e1c2932
Groovy-ngs fixes
Oct 26, 2016
af2e982
Installer working!
Oct 26, 2016
e3a8628
Made all download tasks setup tasks, fixing the reinstallation issue
Oct 26, 2016
b4b7c9b
Fixed data files not downloading correctly
Oct 26, 2016
2dd56bd
Fixed config groovy for nnew setup
Oct 26, 2016
2e0e5c9
Re-added java emulator
Oct 26, 2016
307b9c6
Added execute to java emulator
Oct 26, 2016
ce8659c
More config groovy fixes
Oct 26, 2016
0dfce26
Fixed dbsnp index
Oct 27, 2016
d1e4365
Removed noverify default
Oct 27, 2016
361abf5
Add swift credentials to readme, export TMPDIR
multimeric Oct 28, 2016
9fbe0ed
Update docs, mostly output docs
multimeric Oct 31, 2016
212eaef
Add full names to output docs
multimeric Oct 31, 2016
5909c1d
Add Installation Name instructions
multimeric Oct 31, 2016
efd0723
Fix dependency titles in installation docs
multimeric Oct 31, 2016
c760732
Fix Installation Name title
multimeric Oct 31, 2016
42feead
Newlines for genelist command
multimeric Oct 31, 2016
b08035a
Fix terminal bug in install
multimeric Nov 1, 2016
21d1f21
Fix groovy manual download
multimeric Nov 1, 2016
898b1d2
Update command docs
multimeric Nov 1, 2016
c90afb9
Fixed and added test for manage batch script
multimeric Nov 1, 2016
65522cd
Fixed commands merge conflict
multimeric Nov 1, 2016
f82a09c
Added tables of contents to docs
multimeric Nov 1, 2016
4734a3b
Updated docs; more designs info
multimeric Nov 1, 2016
acfa584
More documentation; add links from readme to relevant docs
multimeric Nov 1, 2016
2a35c6c
Fix metadata table in batches.md
multimeric Nov 1, 2016
41730d2
Better instructions on creating a batch
multimeric Nov 1, 2016
650f38b
Add code blocks to batches.md
multimeric Nov 1, 2016
aec7f8f
Fix wrong link type in batches.md
multimeric Nov 1, 2016
b9b6198
More docs fixes
multimeric Nov 1, 2016
92af917
Merge pull request #190 from MelbourneGenomics/install-rewrite
multimeric Nov 1, 2016
423bafc
Merge pull request #191 from MelbourneGenomics/dev
multimeric Nov 1, 2016
0476905
Stopped massive logging for manage batch test
multimeric Nov 2, 2016
3b592c3
Merge pull request #192 from MelbourneGenomics/dev
multimeric Nov 2, 2016
5e0e1be
Fix reported number of samples being reported as 1 less than reality
multimeric Nov 4, 2016
9e0e7f6
Allow running nested batches
multimeric Nov 6, 2016
7bbb96b
Allow --batch flag after run command
multimeric Nov 7, 2016
d4bc5ac
Documentation additions/fixes: reanalysis, public installer, config.b…
multimeric Nov 7, 2016
06ebc18
Initial docker docs
multimeric Nov 8, 2016
db4fb83
Docker docs small fixes
multimeric Nov 8, 2016
62a0c09
More docker doc fixes
multimeric Nov 8, 2016
204e18e
More docker doc fixes
multimeric Nov 8, 2016
000145a
Added toc to docker docs
multimeric Nov 8, 2016
82a6e79
Docker docs additions; remove python from cpipe commands
multimeric Nov 8, 2016
efe40aa
More docker docs fixes
multimeric Nov 8, 2016
f7bf5f2
Public installer (#193)
multimeric Nov 9, 2016
552fdbc
Fix wrong docker command; encourage aliasing docker run
multimeric Nov 9, 2016
aea53ac
More docker clarifications
multimeric Nov 9, 2016
fc2149a
Update docker.md
multimeric Nov 9, 2016
48d38d3
Update docker.md
multimeric Nov 9, 2016
d5adc23
Update docker.md
multimeric Nov 9, 2016
1191728
updated bpipe.config with more realistic walltimes
supernifty Nov 10, 2016
03e1ec9
warn and continue if a sample has additional columns in qc_report CPI…
supernifty Nov 14, 2016
2eafc88
Merge pull request #194 from MelbourneGenomics/metadata-parsing-qc
supernifty Nov 18, 2016
dab2894
Update version.txt
multimeric Nov 20, 2016
9b0b443
Merge branch 'dev' of github.com:MelbourneGenomics/cpipe into dev
multimeric Nov 20, 2016
a3e4e53
Remove 'batch' as default batch name; prevent 'batch' from ever being…
multimeric Nov 21, 2016
c4bcc27
Fix pip libraries not loading
multimeric Nov 21, 2016
d4d34b6
Add pandas
multimeric Nov 21, 2016
f73876d
Started on manage batch rewrite
multimeric Nov 21, 2016
65d7627
additional metadata field descriptions
supernifty Nov 25, 2016
23ab7f1
Merge pull request #197 from MelbourneGenomics/docs
supernifty Nov 25, 2016
3180c6a
Update batches.md
supernifty Nov 25, 2016
38cd06f
Update batches.md
supernifty Nov 25, 2016
74a64cc
Update batches.md
supernifty Nov 25, 2016
6e06735
More rewriting of manage_batch
multimeric Nov 28, 2016
821f051
Convert pipeline scripts to python 3
multimeric Nov 28, 2016
fcdb29a
Merge branch 'dev' of github.com:MelbourneGenomics/cpipe into dev
multimeric Nov 28, 2016
78c4ce5
Update install tasks to python 3
multimeric Nov 28, 2016
3925abe
Update install script to install python 3
multimeric Nov 28, 2016
11ea7aa
Convert pipeline scripts to python 3 (#198)
multimeric Nov 28, 2016
bd45658
Update cpipe_utility to use pathlib
multimeric Nov 28, 2016
627e185
Merge branch 'python-3' into dev
multimeric Nov 28, 2016
2afc42b
Merge branch 'dev' of github.com:MelbourneGenomics/cpipe into dev
multimeric Nov 28, 2016
772ae00
Move manage batch to a module; finished arg parsing
multimeric Nov 28, 2016
c78364f
Finished basic manage batch implementation
multimeric Nov 29, 2016
b61a807
Validate most columns in validate script
multimeric Nov 30, 2016
befbe3f
Fix install script for python 3
multimeric Nov 30, 2016
0b2cfdd
Fix Cpipe script for new manage batch
multimeric Nov 30, 2016
cefd113
Update errors in 2.4 docs
multimeric Dec 1, 2016
b31a352
Add custom CsvSchema lib
multimeric Dec 2, 2016
d548e11
Fix installer bug being unable to remove temp dir
multimeric Dec 2, 2016
867c637
Fix installer bug being unable to remove temp dir (#199)
multimeric Dec 2, 2016
9a0b3eb
Fix merge conflicts
multimeric Dec 2, 2016
b7e0fb9
support for additional annotation with ExAC and 1000G
supernifty Dec 8, 2016
e7b6f4b
support separate annotation with ExAC and 1000Gp3
supernifty Dec 8, 2016
9620ed6
Merge pull request #201 from MelbourneGenomics/af-annotation
supernifty Dec 8, 2016
ca6d545
additional dbnsfp fields, remove redundant exac/1000g fields
supernifty Dec 14, 2016
83cc2bc
Merge pull request #202 from MelbourneGenomics/af-annotation
supernifty Dec 14, 2016
5bd2555
Finished validation using pandas_schema, editing using visidata
multimeric Jan 5, 2017
4c42f84
Python 3.6, Batch class improvements, manage batch work
multimeric Jan 6, 2017
6ba1585
Finish moving Batch methods from manage_batch into Batch class
multimeric Jan 9, 2017
8e50805
Fix python 3 errors with tests, finished tests for manage batch
multimeric Jan 9, 2017
7fe4afe
Pipeline ID task
multimeric Jan 11, 2017
f7f7d45
increase memory requirement for check_coverage stage
supernifty Jan 12, 2017
dc83b35
Merge branch 'dev' of https://github.com/MelbourneGenomics/cpipe into…
supernifty Jan 12, 2017
746c1bf
Working package install
multimeric Jan 12, 2017
3f28e5f
Rework python package, binary symlinks
multimeric Jan 16, 2017
0a47b52
Use entry_points instead of scripts, rewrite cpipe run script in python
multimeric Feb 3, 2017
d877ce6
Convert ./cpipe to python
multimeric Mar 17, 2017
2afda91
More package changes
multimeric Mar 21, 2017
b0dae95
More package changes
multimeric Mar 21, 2017
d299b6a
Fix setup py to not import cpipe
multimeric Mar 22, 2017
175f0f6
Fixed c_libs install and cpipe run script
Mar 22, 2017
131cfbf
Unit tests working
Apr 4, 2017
7934828
Use our ngs-utils
multimeric Apr 4, 2017
fe550cd
Update manual download tasks; make build.gradle for java libs
Apr 6, 2017
1218f35
Use gradle for java libs, don't install them individually
Apr 10, 2017
a4a2073
Fixes for manual install; add cpipe bpipe command
Apr 20, 2017
91e2b45
Fix dependency clashes for gradle
Apr 21, 2017
9f56a0b
Fix infinite java loop (CPIPE-215)
Apr 21, 2017
6d2187b
Move non-python scripts back to root directory
Apr 21, 2017
ab1b9dc
Add basic development docs
Apr 21, 2017
c884fb0
Update development.md
multimeric Apr 21, 2017
8088b9d
Fixed vep API installation
Apr 24, 2017
172409f
Merge branch 'python-package' of https://github.com/MelbourneGenomics…
Apr 24, 2017
9dc82a4
Index vep cache
May 4, 2017
a4028e7
Add upload_assets script to main cpipe repo
May 4, 2017
c5998c2
Update nectar assets
May 4, 2017
a7cd500
Environment file now starts new shell
May 4, 2017
f6781df
Update vep_plugins
May 5, 2017
71d0ae1
Installer fixed
May 5, 2017
8d53300
Merge branch 'python-package' of https://github.com/MelbourneGenomics…
May 5, 2017
3bdb4fb
Added container to vep_plugins
May 5, 2017
3c2b84f
More installer fixes
May 8, 2017
b98a96d
More installer fixes
May 9, 2017
99b7325
Prompt user for queuing system
May 9, 2017
3d64df2
Fixed java lib installation
May 10, 2017
6dadbc1
Merge branch 'python-package' of https://github.com/MelbourneGenomics…
May 10, 2017
b070f71
Fixed java check
May 11, 2017
20a8e48
Remove sample database update
May 11, 2017
ee154ac
Fixed bpipe config template for torque
May 11, 2017
2f6ca94
Merge branch 'python-package' of https://github.com/MelbourneGenomics…
May 11, 2017
b1de75f
Separated bpipe config generator into separate script; improved it
May 11, 2017
53bcfa7
Fix bpipe creation script
multimeric May 25, 2017
c219e36
Merge pull request #208 from MelbourneGenomics/python-package
multimeric May 25, 2017
e3fd54b
Merge branch '2.4' of github.com:MelbourneGenomics/cpipe into python-…
multimeric May 25, 2017
4c3f7a5
Merge branch 'dev' of github.com:MelbourneGenomics/cpipe into python-…
multimeric May 25, 2017
2647686
Fix VCFAnno install; fix bpipe_config creator script
May 30, 2017
642afa8
Fixed batch sex validation; Started 2.5 documentation
multimeric May 30, 2017
3aa1835
Improved java check
Jun 1, 2017
6f9b473
Merge branch 'dev' of https://github.com/MelbourneGenomics/cpipe into…
Jun 1, 2017
a79400b
Update batch docs
multimeric Jun 1, 2017
1868410
Documentation updates, CLI fixes
multimeric Jun 1, 2017
a4174b0
Update document tables of contents
multimeric Jun 1, 2017
43de02f
Updated Docker docs
multimeric Jun 2, 2017
f32f14d
Fixed docker.md list
multimeric Jun 2, 2017
c84f962
More numbering fixes
multimeric Jun 2, 2017
5e7b060
Merge branch 'dev' of github.com:MelbourneGenomics/cpipe into dev
multimeric Jun 2, 2017
1c97a8c
Docker TOC
multimeric Jun 2, 2017
76d0e21
Installer fixes
Jun 2, 2017
39add69
Fix picard install
Jun 2, 2017
34b6d18
Updated variants in outputs.md
multimeric Jun 2, 2017
0d202a4
Merge branch 'dev' of github.com:MelbourneGenomics/cpipe into dev
multimeric Jun 2, 2017
a4a4ac2
Documentation updates
Jun 5, 2017
a0c7a27
Update README.md
multimeric Jun 5, 2017
21e88b6
Update commands.md
multimeric Jun 5, 2017
a592dce
Added md5 validation, improved batch create command, updated docs
Jun 5, 2017
aa88b34
Merge branch 'dev' of https://github.com/MelbourneGenomics/cpipe into…
Jun 5, 2017
104dc36
Re-added Visidata documentation
Jun 5, 2017
a131ce8
Update commands.md
multimeric Jun 5, 2017
ac6961f
Updated vep plugin commit
Jun 13, 2017
c7582e9
Fixed Grantham VEP plugin
Jun 15, 2017
740faa8
Attemped fix for md5 sum
Jun 15, 2017
94d75d5
Permission error docs
Jun 15, 2017
c0fd620
Add cpipe stop command
Jun 15, 2017
accd97e
Update bpipe to 0.9.9.4
Jun 15, 2017
5e89d86
Update troubleshooting.md
multimeric Jun 15, 2017
1e57521
Updated development docs
Jun 15, 2017
3844759
Update index.md
multimeric Jun 15, 2017
9e55e2f
Rename environment to 'cpipe'
Jun 15, 2017
6374a66
Fix cpipe script
multimeric Jun 15, 2017
4f5550f
Update -NOVERIFY flag documentation
Jun 15, 2017
15d2edd
Merge branch 'dev' of https://github.com/MelbourneGenomics/cpipe into…
Jun 15, 2017
d278ba3
Fix cpipe test
Jun 16, 2017
9eb0d23
Fix CLI scripts
Jun 16, 2017
03daa00
Document ./cpipe command rather than ./environment.sh
Jun 19, 2017
1759c67
Improved Docker docs
Jun 19, 2017
38092bc
Update docker.md
multimeric Jun 19, 2017
b6ee0c4
Update docker.md
multimeric Jun 19, 2017
f479674
Update README.md
multimeric Jun 20, 2017
793b017
Update README.md
multimeric Jun 20, 2017
3808aab
Fixed installer help
Jun 20, 2017
20bd7bd
Merge branch 'dev' of https://github.com/MelbourneGenomics/cpipe into…
Jun 20, 2017
e043446
Update install.md
multimeric Jun 20, 2017
af9143e
Update install.md
multimeric Jun 20, 2017
9d45d3a
Fixed install.md TOC
Jun 27, 2017
daa35c8
Merge branch 'dev' of https://github.com/MelbourneGenomics/cpipe into…
Jun 27, 2017
062abf1
Lock down pip package versions
Jul 17, 2017
a84ea43
Merge branch 'dev' of https://github.com/MelbourneGenomics/cpipe into…
Jul 17, 2017
92628fc
Update docker.md
multimeric Jul 18, 2017
cf06701
Fix race condition that `doit` tasks fail to update manifest file
biocyberman Jan 11, 2018
48e420e
Make lock work correctly
biocyberman Jan 12, 2018
86a072c
Put back install perl_libs
biocyberman Jan 12, 2018
a2a1453
Merge pull request #215 from aalborguh/pr
multimeric Jan 20, 2018
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16 changes: 16 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -1,2 +1,18 @@
/tools/
/data/
/pipeline/config.groovy
/tasks/nectar/current.manifest.json
samples.db
pipeline_id
swift_credentials.sh
**.doit.db
.idea
.bpipe
*.pyc
*.swp
tmpdata
batches
!designs/ALL
**.log
**.bak
lib/*.egg-info/
19 changes: 19 additions & 0 deletions Dockerfile
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
FROM ubuntu

# Start using bash
SHELL ["/bin/bash", "-c"]

# Install basic linux tools that we need to make python
RUN apt-get update && apt-get install -y curl make build-essential libssl-dev zlib1g-dev libsqlite3-dev libreadline-dev git libbz2-dev libz-dev libssl-dev gfortran xorg-dev libcurl4-openssl-dev ncurses-dev openjdk-8-jdk

# Copy in the repository
ADD . /opt/cpipe

# Move into the cpipe dir
WORKDIR /opt/cpipe

# Run the install script
RUN ./install.sh --noninteractive

# Run the main script
ENTRYPOINT ["./cpipe"]
32 changes: 28 additions & 4 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,16 +1,40 @@
Cpipe
=======================
# Cpipe

Cpipe is a clinically focused exome sequencing pipeline developed
by the Melbourne Genomics Health Alliance. Cpipe offers an industry
standard variant calling pipeline with a suite of additional features
needed by diagnostic laboratories added on top.

A simplified workflow is presented here. For more specific information, refer to the [documentation](docs/index.md).

## Installation

To set up Cpipe, clone this repository and then run the install script:

git clone https://github.com/MelbourneGenomics/cpipe.git
cd cpipe
./pipeline/scripts/install.sh
./install.sh

Ensure you follow any instructions given by the install script. For example, non MGHA users must install their own
version of GATK since their license forbids us from redistributing it.

For more detailed instructions, have a look at the [installation documentation](docs/install.md).

## Creating your analysis batch
* First, rename your fastqs to ensure they fit the following pattern:
`sampleID_<anything>_L[0-9]*_R[0-9].fastq.gz`
* Tell Cpipe to create a new batch using your fastq files
```bash
./cpipe batch create MyBatch --data path/to/samples/*.fastq.gz --exome path/to/exons.bed
```
* `MyBatch` is the batch name
* `path/to/exons.bed` is the filepath to a capture regions bed file specified by your sequencer
* `path/to/samples/*.fastq.gz` is the filepath to the sample fastqs you want to put in your batch

For more information about this stage, refer to the [batches documentation](docs/batches.md).

## Running the Pipeline

For further instructions, take a look at the [User Guide](https://melbournegenomics.github.io/docs/Cpipe_User_Guide.pdf).
Now, all you need to do is run `./cpipe run MyBatch`

The run command is documented in the [command documentation](docs/commands.md#run).
56 changes: 56 additions & 0 deletions _env
Original file line number Diff line number Diff line change
@@ -0,0 +1,56 @@
#!/usr/bin/env bash
# Local variables

# Util functions
function join() {
local IFS=$1
shift
echo "$*"
}

function load_config {
CONFIG=`sed 's/\/\/.*$//' $CONFIG_FILE`
eval "$CONFIG"
}

function set_config_variable {
NAME="$1"
VALUE="$2"
cp "$CONFIG_FILE" "$CONFIG_FILE.tmp"
sed 's,'^[\s]*$NAME'=\("\?\).*$,'$NAME'=\1'$VALUE'\1,g' ${CONFIG_FILE}.tmp > "$CONFIG_FILE"
rm "${CONFIG_FILE}.tmp"
load_config
}

# Work out the directory name
if [ -n "$ZSH_VERSION" ]; then
ROOT=$(readlink -f $(dirname $0))
else
ROOT=$(readlink -f $(dirname $BASH_SOURCE))
fi

# Set root variables
export CPIPE_ROOT=${ROOT}
CONFIG_FILE=${CPIPE_ROOT}/pipeline/config.groovy

# Load config groovy
if [[ -f ${CONFIG_FILE} ]] ; then
load_config
fi

# Add all tool directories and bin folders to PATH
export SYS_JAVA=`which -a java | grep -v -m1 'cpipe'` # Export the old system java before we override it
export PATH=${TOOLS}/bin:${TOOLS}/maven/bin:${TOOLS}/bpipe/bin:${PATH}
export HTSLIB_DIR=$TOOLS/lib
export PERL5LIB=$TOOLS/perl_lib/lib/perl5:$TOOLS/perl/lib:$TOOLS/vep_plugins:${TOOLS}/vep_libs
export CPATH="${TOOLS}/include"
export CFLAGS="$CFLAGS -I${TOOLS}/include"
export CPPFLAGS="$CPPFLAGS -I${TOOLS}/include"
export LDFLAGS="$LDFLAGS -L${TOOLS}/lib"
export LD_LIBRARY_PATH=${TOOLS}/lib:${LD_LIBRARY_PATH}
export JAVA_OPTS #Pass JAVA_OPTS to the script in c_libs/bin/java
export TMPDIR #TMPDIR is set in config.groovy.

# Load virtualenv
source ${CPIPE_ROOT}/tools/python/bin/activate

8 changes: 0 additions & 8 deletions bpipe

This file was deleted.

42 changes: 42 additions & 0 deletions build.gradle
Original file line number Diff line number Diff line change
@@ -0,0 +1,42 @@
apply plugin:'java'
apply plugin: 'maven'
group = 'com.github.MelbourneGenomics'

repositories {
mavenCentral()
maven { url 'https://jitpack.io' }
maven {
name "biojava"
url "http://www.biojava.org/download/maven/"
}
maven {
name "gral"
url "http://mvn.erichseifert.de/maven2"
}
mavenLocal()
maven {
url "https://artifactory.broadinstitute.org/artifactory/libs-snapshot/" //for htsjdk snapshots
}
}

//configurations.all {
// transitive false
//}

dependencies {
compile 'com.github.MelbourneGenomics:groovy-hts-sample-info:562ba2a64e8@jar'
compile 'com.github.ssadedin:groovy-ngs-utils:d6fdc538d9b@jar'
compile 'com.github.barrypitman:JUnitXmlFormatter:9893370f4112@jar'
compile 'io.takari.junit:takari-cpsuite:1.2.7@jar'
//compile 'com.github.broadinstitute:picard:2.9.0'
//compile 'com.github.ssadedin:bpipe:0.9.9.2@jar'
//compile 'com.github.broadgsa:gatk-protected:3.6'
}

task copyDeps(type: Copy) {
// Use `gradle copyDeps -Pdir=/some/dir to specify where to puts the jars`
from configurations.runtime
exclude '**/*picard.jar', '**/*groovy-*-2.*.*.jar', '**/*groovy-2.*.*.jar'
into project.hasProperty('dir') ? project.property('dir') : 'tools/java_libs'
//rename '(.*)-[a-z0-9\\.]+.jar', '$1.jar'
}
9 changes: 9 additions & 0 deletions cpanfile
Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
requires 'HTTP::Tiny', '== 0.056';
requires 'LWP::Simple', '== 6.15';
requires 'Archive::Zip', '== 1.56';
requires 'DBI', '== 1.636';
requires 'LWP::Protocol::https', '== 6.04';
requires 'File::Copy::Recursive', '== 0.38';
requires 'Archive::Extract', '== 0.78';
requires 'CGI', '== 4.32';
requires 'Bio::DB::HTS', '== 2.4';
14 changes: 14 additions & 0 deletions cpipe
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
#!/bin/bash

REMAINDER="${@:1}"
ROOT=`dirname $0`
ENV_SCRIPT="$ROOT/_env"

if [[ -n $REMAINDER ]]; then
# If the user provided arguments, run the cpipe command using those arguments
source $ENV_SCRIPT
cpipe $REMAINDER
else
# If the user provided no arguments, start a new subshell, set variables in that, and then give control back to the user. They can then quit using Ctrl+D
bash --init-file "${ROOT}/_env"
fi
26,369 changes: 26,369 additions & 0 deletions designs/ALL/ALL.genes.txt

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