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Some bugfixes for the installation process #211

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Some bugfixes for the installation process #211

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ccd4156
Fixed missing download types, and gave more informative error messages
biocyberman Oct 30, 2017
ab9f0f9
Avoided error with accidental deletion of `tmpdata`
biocyberman Oct 30, 2017
ea8ef24
Fixed missing field of action's return in `task_download_cpanm`
biocyberman Oct 30, 2017
9ce8981
Fixed a typo for index command in `task_bwa_index_ucsc_reference`.
biocyberman Oct 30, 2017
ba286e9
Unziped ucsc hg19 genome so tools that expect `.fasta` can run
biocyberman Oct 30, 2017
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1 change: 1 addition & 0 deletions install.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ set -e
PYTHON_VERSION='3.6.0'
PYTHON_INTERPRETER='python3.6'
ROOT=$(readlink -f $(dirname ${BASH_SOURCE}))
mkdir -p ${ROOT}/tmpdata
export TMPDIR=${ROOT}/tmpdata # Write temporary files to tmpdata
export CPIPE_ROOT=$ROOT
TEMP_SUBDIR=`mktemp -d`
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7 changes: 5 additions & 2 deletions tasks/common.py
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Expand Up @@ -163,7 +163,7 @@ def unzip_todir(input, directory, type):
tar = tarfile.open(fileobj=input, mode='r:bz2')
tar.extractall(tempdir)
else:
raise ValueError('Can only download .tar.gz, .tar.bz2, or .zip file')
raise ValueError('Type: {0} given. Can only download .tar.gz, .tar.bz2, or .zip file'.format(type))

# If there is only one subdirectory, take the files inside that
files = [os.path.join(tempdir, f) for f in os.listdir(tempdir)]
Expand Down Expand Up @@ -207,7 +207,7 @@ def download_zip(url_str, directory, type=None):
input = BytesIO(url.read())

# Try to deduce the type from the URL
if not type:
if type is None:
[name, ext2] = os.path.splitext(url_str)
[name, ext1] = os.path.splitext(name)

Expand All @@ -217,6 +217,9 @@ def download_zip(url_str, directory, type=None):
type = 'tgz'
elif (ext1 == '.tar' and ext2 == '.bz2') or ext2 == '.tbz2':
type = 'tbz2'
else:
raise ValueError ("Unknow filetype: ext1: {}, ext2: {}\nurl_str: {}".format(ext1, ext2,
url_str))

unzip_todir(input, directory, type)

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12 changes: 10 additions & 2 deletions tasks/download/download_reference_files.py
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Original file line number Diff line number Diff line change
Expand Up @@ -130,7 +130,15 @@ def task_download_ucsc():
["ucsc.hg19.dict.gz", "ucsc.hg19.fasta.gz", "ucsc.hg19.fasta.fai.gz"],
UCSC_ROOT,
'bundle/hg19/'
)
),
cmd('''
mkdir -p ucsc\
&& pushd {data_dir}/ucsc\
&& gunzip -c ucsc.hg19.dict.gz >ucsc.hg19.dict\
&& gunzip -c ucsc.hg19.fasta.fai.gz >ucsc.hg19.fasta.fai\
&& gunzip -c ucsc.hg19.fasta.gz >ucsc.hg19.fasta
'''.format(data_dir=DATA_ROOT), cwd=DATA_ROOT, executable='bash')

],
'uptodate': [run_once],
}
Expand Down Expand Up @@ -311,7 +319,7 @@ def task_bwa_index_ucsc_reference():
return {
'targets': [UCSC_BWA_INDEX],
'actions': [
'{tools}/bwa/bwa index -a bwtsw {data}/ucsc/ucsc.hg19.fasta'.format(tools=TOOLS_ROOT, data=DATA_ROOT)
'{tools}/bin/bwa index -a bwtsw {data}/ucsc/ucsc.hg19.fasta'.format(tools=TOOLS_ROOT, data=DATA_ROOT)
],
'task_dep': [
'install_bwa',
Expand Down
9 changes: 6 additions & 3 deletions tasks/download/download_tools.py
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Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,9 @@ def action():
curl -L https://cpanmin.us/ -o cpanm
chmod +x cpanm
''', cwd=temp_dir)
return {
'dir': temp_dir
}

return {
'actions': [action],
Expand Down Expand Up @@ -99,7 +102,7 @@ def task_download_bwa():
if swift_install():
return nectar_download('bwa')
else:
return download_task("https://codeload.github.com/lh3/bwa/tar.gz/v{0}".format(BWA_VERSION))
return download_task("https://codeload.github.com/lh3/bwa/tar.gz/v{0}".format(BWA_VERSION), type='tgz')


def task_download_htslib():
Expand Down Expand Up @@ -130,7 +133,7 @@ def task_download_bedtools():
if swift_install():
return nectar_download('bedtools')
else:
return download_task("https://codeload.github.com/arq5x/bedtools2/tar.gz/v{0}".format(BEDTOOLS_VERSION))
return download_task("https://codeload.github.com/arq5x/bedtools2/tar.gz/v{0}".format(BEDTOOLS_VERSION), type='tgz')

def task_download_vep():
if swift_install():
Expand Down Expand Up @@ -331,7 +334,7 @@ def task_download_zlib():
return nectar_download('zlib')
else:
return download_task(
'https://codeload.github.com/madler/zlib/tar.gz/v{}'.format(ZLIB_VERSION))
'https://codeload.github.com/madler/zlib/tar.gz/v{}'.format(ZLIB_VERSION), type='tgz')

def task_download_vcfanno():
if has_swift_auth():
Expand Down