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v0.3.0
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@golobor
golobor committed Jan 2, 2019
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13 changes: 13 additions & 0 deletions CHANGES.md
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### 0.3.0 (2019-01-02) ###

A major update of the pipeline and the config syntax.
* Simplify and speed up the pipeline by merging several groups of processes.
* Greatly reduce the storage requirements down to ~2x of the fastq.gz size.
* Introduce custom pair filtering during binning.
* Make .mcools with custom resolutions.
* Speed up the .sra->.fastq.gz conversion.
* Rename multiple config options.
* Switch from pbgzip to native bgzip multithreading.
* Allow users to change the location of the temp files.
* Post the list of the packages inside the docker on github.

### 0.2.0 (2018-11-18) ###

* report mapq in .pairs
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2 changes: 1 addition & 1 deletion VERSION
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version='0.2.0'
version='0.3.0'
57,431 changes: 57,431 additions & 0 deletions docker/apt.list
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2 changes: 2 additions & 0 deletions docker/build.sh
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trap cleanup EXIT

docker build -t $USERNAME/$IMAGE:latest .
docker run -it mirnylab/distiller_env:latest apt list > ./apt.list
docker run -it mirnylab/distiller_env:latest conda list > ./conda.list
110 changes: 110 additions & 0 deletions docker/conda.list
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# packages in environment at /miniconda3:
#
# Name Version Build Channel
asciitree 0.3.3 <pip>
asn1crypto 0.24.0 py36_1003 conda-forge
biopython 1.73 <pip>
blas 1.1 openblas conda-forge
bokeh 1.0.2 py36_1000 conda-forge
bwa 0.7.17 ha92aebf_3 bioconda
bzip2 1.0.6 h470a237_2 conda-forge
ca-certificates 2018.11.29 ha4d7672_0 conda-forge
certifi 2018.11.29 py36_1000 conda-forge
cffi 1.11.5 py36h5e8e0c9_1 conda-forge
chardet 3.0.4 py36_1003 conda-forge
click 7.0 py_0 conda-forge
cloudpickle 0.6.1 py_0 conda-forge
conda 4.5.12 py36_1000 conda-forge
conda-env 2.6.0 1
cooler 0.8.0 <pip>
coreutils 8.30 h470a237_0 conda-forge
cryptography 2.3.1 py36hdffb7b8_0 conda-forge
cryptography-vectors 2.3.1 py36_1000 conda-forge
curl 7.63.0 h74213dd_0 conda-forge
cython 0.29.2 py36hfc679d8_0 conda-forge
cytoolz 0.9.0.1 py36h470a237_1 conda-forge
dask 1.0.0 py_0 conda-forge
dask-core 1.0.0 py_0 conda-forge
dill 0.2.8.2 <pip>
distributed 1.25.1 py36_1000 conda-forge
fastqc 0.11.8 1 bioconda
font-ttf-dejavu-sans-mono 2.37 h6964260_0
fontconfig 2.13.1 h65d0f4c_0 conda-forge
freetype 2.9.1 h6debe1e_4 conda-forge
h5py 2.9.0 <pip>
heapdict 1.0.0 py36_1000 conda-forge
htslib 1.9 hc238db4_4 bioconda
icu 58.2 hfc679d8_0 conda-forge
idna 2.8 py36_1000 conda-forge
jinja2 2.10 py_1 conda-forge
jpeg 9c h470a237_1 conda-forge
krb5 1.16.2 hbb41f41_0 conda-forge
libcurl 7.63.0 hbdb9355_0 conda-forge
libdeflate 1.0 h470a237_0 bioconda
libedit 3.1.20170329 h6b74fdf_2
libffi 3.2.1 hd88cf55_4
libgcc-ng 8.2.0 hdf63c60_1
libgfortran 3.0.0 1 conda-forge
libiconv 1.15 h470a237_3 conda-forge
libpng 1.6.36 ha92aebf_0 conda-forge
libssh2 1.8.0 h5b517e9_3 conda-forge
libstdcxx-ng 8.2.0 hdf63c60_1
libtiff 4.0.10 he6b73bb_1 conda-forge
libuuid 2.32.1 h470a237_2 conda-forge
libxml2 2.9.8 h422b904_5 conda-forge
locket 0.2.0 py_2 conda-forge
lz4-c 1.8.3 hfc679d8_0 conda-forge
markupsafe 1.1.0 py36h470a237_0 conda-forge
msgpack-python 0.6.0 py36h2d50403_0 conda-forge
multiprocess 0.70.6.1 <pip>
ncurses 6.1 hf484d3e_0
nose 1.3.7 py36_1002 conda-forge
numpy 1.15.4 py36_blas_openblashb06ca3d_0 [blas_openblas] conda-forge
olefile 0.46 py_0 conda-forge
openblas 0.3.3 ha44fe06_1 conda-forge
openjdk 11.0.1 h470a237_14 conda-forge
openssl 1.0.2p h470a237_1 conda-forge
packaging 18.0 py_0 conda-forge
pairix 0.3.6 py36ha92aebf_2 bioconda
pairtools 0.2.1 py36he8651fa_0 bioconda
pandas 0.23.4 py36hf8a1672_0 conda-forge
parallel 20181022 0 conda-forge
partd 0.3.9 py_0 conda-forge
pbgzip 2016.08.04 he4cf2ce_0 bioconda
perl 5.26.2 h470a237_0 conda-forge
pillow 5.3.0 py36hc736899_0 conda-forge
pip 18.1 py36_1000 conda-forge
psutil 5.4.8 py36h470a237_0 conda-forge
pycosat 0.6.3 py36h470a237_1 conda-forge
pycparser 2.19 py_0 conda-forge
pyfaidx 0.5.5.2 <pip>
pyopenssl 18.0.0 py36_1000 conda-forge
pyparsing 2.3.0 py_0 conda-forge
pysam 0.15.1 <pip>
pysocks 1.6.8 py36_1002 conda-forge
python 3.6.7 h5001a0f_1 conda-forge
python-dateutil 2.7.5 py_0 conda-forge
pytz 2018.7 py_0 conda-forge
pyyaml 3.13 py36h470a237_1 conda-forge
readline 7.0 h7b6447c_5
requests 2.21.0 py36_1000 conda-forge
ruamel_yaml 0.15.71 py36h470a237_0 conda-forge
samtools 1.9 h8ee4bcc_1 bioconda
scipy 1.2.0 <pip>
seqtk 1.3 ha92aebf_0 bioconda
setuptools 40.6.3 py36_0 conda-forge
six 1.12.0 py36_1000 conda-forge
sortedcontainers 2.1.0 py_0 conda-forge
sqlite 3.26.0 h7b6447c_0
sra-tools 2.9.1_1 h470a237_0 bioconda
tabix 0.2.6 ha92aebf_0 bioconda
tblib 1.3.2 py_1 conda-forge
tk 8.6.9 ha92aebf_0 conda-forge
toolz 0.9.0 py_1 conda-forge
tornado 5.1.1 py36h470a237_0 conda-forge
urllib3 1.24.1 py36_1000 conda-forge
wheel 0.32.3 py36_0 conda-forge
xz 5.2.4 h14c3975_4
yaml 0.1.7 had09818_2
zict 0.1.3 py_0 conda-forge
zlib 1.2.11 ha838bed_2
2 changes: 1 addition & 1 deletion project.yml
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# {filter_name}: '{a valid Python expression}'
filters:
no_filter: ''
mapq_30: '(int(mapq1)>=30) and (int(mapq2)>=30)'
mapq_30: '(mapq1>=30) and (mapq2>=30)'

########################################
# folder structure for storing results
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2 changes: 1 addition & 1 deletion test/test_project.yml
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# {filter_name}: '{a valid Python expression}'
filters:
no_filter: ''
mapq_30: '(int(mapq1)>=30) and (int(mapq2)>=30)'
mapq_30: '(mapq1>=30) and (mapq2>=30)'


########################################
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