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Setting up falconUnzip conda environments for genome assembly !
By Jit 1981 days ago
➜ Analysis_Results conda create -n denovo_asm
Solving environment: done
## Package Plan ##
environment location: /home/urbe/anaconda3/envs/denovo_asm
Proceed ([y]/n)? y
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
# $ conda activate denovo_asm
#
# To deactivate an active environment, use
#
# $ conda deactivate
➜ Analysis_Results source activate denovo_asm
(denovo_asm) ➜ Analysis_Results conda install pb-assembly
Solving environment: done
## Package Plan ##
environment location: /home/urbe/anaconda3/envs/denovo_asm
added / updated specs:
- pb-assembly
The following packages will be downloaded:
package | build
---------------------------|-----------------
python-2.7.15 | h33da82c_5 13.6 MB conda-forge
pysam-0.14.1 | py27hae42fb6_1 7.2 MB bioconda
pb-dazzler-0.0.0 | h470a237_0 755 KB bioconda
cryptography-vectors-2.3.1 | py27_1000 30.5 MB conda-forge
requests-2.20.1 | py27_1000 83 KB conda-forge
setuptools-40.6.2 | py27_0 622 KB conda-forge
avro-python2-1.8.2 | py_1 30 KB bioconda
python-sortedcontainers-2.0.5| py_0 25 KB bioconda
genomicconsensus-2.3.2 | py27_3 97 KB bioconda
python-consensuscore2-3.1.0| py27_2 848 KB bioconda
enum34-1.1.6 | py27_1001 56 KB conda-forge
chardet-3.0.4 | py27_1003 180 KB conda-forge
pyopenssl-18.0.0 | py27_1000 78 KB conda-forge
linecache2-1.0.0 | py_1 13 KB conda-forge
urllib3-1.23 | py27_1001 150 KB conda-forge
pycparser-2.19 | py_0 87 KB conda-forge
python-consensuscore-1.1.1 | py27h02d93b8_2 1.4 MB bioconda
pytz-2018.7 | py_0 226 KB conda-forge
cryptography-2.3.1 | py27hdffb7b8_0 964 KB conda-forge
python-edlib-1.2.3.post1 | py27h470a237_0 135 KB bioconda
pbcore-1.6.5 | py27_0 9.7 MB bioconda
pysocks-1.6.8 | py27_1002 22 KB conda-forge
cython-0.29 | py27hfc679d8_0 4.3 MB conda-forge
future-0.17.0 | py27_1000 708 KB conda-forge
ipaddress-1.0.22 | py_1 18 KB conda-forge
pb-assembly-0.0.2 | py27_0 4 KB bioconda
six-1.11.0 | py27_1001 20 KB conda-forge
h5py-2.8.0 | py27h7eb728f_3 1.1 MB conda-forge
asn1crypto-0.24.0 | py27_1003 154 KB conda-forge
cffi-1.11.5 | py27h5e8e0c9_1 388 KB conda-forge
pb-falcon-0.2.4 | py27ha92aebf_0 716 KB bioconda
python-msgpack-0.5.6 | py27h470a237_0 282 KB bioconda
unittest2-1.1.0 | py_0 68 KB conda-forge
minimap2-2.14 | ha92aebf_0 2.0 MB bioconda
mkl-2018.0.3 | 1 198.7 MB
python-intervaltree-2.1.0 | py_0 22 KB bioconda
pbcommand-1.1.1 | py27_2 193 KB bioconda
nim-falcon-0.0.0 | 0 271 KB bioconda
iso8601-0.1.12 | py_1 9 KB conda-forge
pbalign-0.3.1 | py27_1 76 KB bioconda
mummer4-4.0.0beta2 | pl526hfc679d8_3 1.3 MB bioconda
mkl_random-1.0.2 | py27_0 1.0 MB conda-forge
wheel-0.32.3 | py27_0 34 KB conda-forge
intel-openmp-2019.1 | 144 885 KB
traceback2-1.4.0 | py27_0 28 KB conda-forge
idna-2.7 | py27_1002 131 KB conda-forge
sqlite-3.25.3 | hb1c47c0_0 1.6 MB conda-forge
------------------------------------------------------------
Total: 280.6 MB
The following NEW packages will be INSTALLED:
asn1crypto: 0.24.0-py27_1003 conda-forge
avro-python2: 1.8.2-py_1 bioconda
bcftools: 1.9-h4da6232_0 bioconda
bedtools: 2.27.1-he941832_2 bioconda
blas: 1.0-mkl
blasr: 5.3.2-hac9d22c_3 bioconda
blasr_libcpp: 5.3.1-hac9d22c_2 bioconda
bwa: 0.7.17-ha92aebf_3 bioconda
bzip2: 1.0.6-h470a237_2 conda-forge
ca-certificates: 2018.10.15-ha4d7672_0 conda-forge
certifi: 2018.10.15-py27_1000 conda-forge
cffi: 1.11.5-py27h5e8e0c9_1 conda-forge
chardet: 3.0.4-py27_1003 conda-forge
cryptography: 2.3.1-py27hdffb7b8_0 conda-forge
cryptography-vectors: 2.3.1-py27_1000 conda-forge
curl: 7.62.0-h74213dd_0 conda-forge
cython: 0.29-py27hfc679d8_0 conda-forge
decorator: 4.3.0-py_0 conda-forge
enum34: 1.1.6-py27_1001 conda-forge
future: 0.17.0-py27_1000 conda-forge
genomicconsensus: 2.3.2-py27_3 bioconda
h5py: 2.8.0-py27h7eb728f_3 conda-forge
hdf5: 1.10.2-hc401514_2 conda-forge
htslib: 1.7-0 bioconda
idna: 2.7-py27_1002 conda-forge
intel-openmp: 2019.1-144
ipaddress: 1.0.22-py_1 conda-forge
iso8601: 0.1.12-py_1 conda-forge
krb5: 1.16.2-hbb41f41_0 conda-forge
libcurl: 7.62.0-hbdb9355_0 conda-forge
libdeflate: 1.0-h470a237_0 bioconda
libedit: 3.1.20170329-haf1bffa_1 conda-forge
libffi: 3.2.1-hfc679d8_5 conda-forge
libgcc: 7.2.0-h69d50b8_2 conda-forge
libgcc-ng: 7.2.0-hdf63c60_3 conda-forge
libgfortran: 3.0.0-1 conda-forge
libgfortran-ng: 7.2.0-hdf63c60_3 conda-forge
libssh2: 1.8.0-h5b517e9_3 conda-forge
libstdcxx-ng: 7.2.0-hdf63c60_3 conda-forge
linecache2: 1.0.0-py_1 conda-forge
minimap2: 2.14-ha92aebf_0 bioconda
mkl: 2018.0.3-1
mkl_fft: 1.0.6-py27_0 conda-forge
mkl_random: 1.0.2-py27_0 conda-forge
mummer4: 4.0.0beta2-pl526hfc679d8_3 bioconda
ncurses: 6.1-hfc679d8_1 conda-forge
networkx: 2.2-py_1 conda-forge
nim-falcon: 0.0.0-0 bioconda
numpy: 1.15.0-py27h1b885b7_0
numpy-base: 1.15.0-py27h3dfced4_0
openssl: 1.0.2p-h470a237_1 conda-forge
pb-assembly: 0.0.2-py27_0 bioconda
pb-dazzler: 0.0.0-h470a237_0 bioconda
pb-falcon: 0.2.4-py27ha92aebf_0 bioconda
pbalign: 0.3.1-py27_1 bioconda
pbbam: 0.18.0-h1310cd9_1 bioconda
pbcommand: 1.1.1-py27_2 bioconda
pbcore: 1.6.5-py27_0 bioconda
perl: 5.26.2-h470a237_0 conda-forge
pip: 18.1-py27_1000 conda-forge
pycparser: 2.19-py_0 conda-forge
pyopenssl: 18.0.0-py27_1000 conda-forge
pysam: 0.14.1-py27hae42fb6_1 bioconda
pysocks: 1.6.8-py27_1002 conda-forge
python: 2.7.15-h33da82c_5 conda-forge
python-consensuscore: 1.1.1-py27h02d93b8_2 bioconda
python-consensuscore2: 3.1.0-py27_2 bioconda
python-edlib: 1.2.3.post1-py27h470a237_0 bioconda
python-intervaltree: 2.1.0-py_0 bioconda
python-msgpack: 0.5.6-py27h470a237_0 bioconda
python-sortedcontainers: 2.0.5-py_0 bioconda
pytz: 2018.7-py_0 conda-forge
readline: 7.0-haf1bffa_1 conda-forge
requests: 2.20.1-py27_1000 conda-forge
samtools: 1.9-h8ee4bcc_1 bioconda
setuptools: 40.6.2-py27_0 conda-forge
six: 1.11.0-py27_1001 conda-forge
sqlite: 3.25.3-hb1c47c0_0 conda-forge
tk: 8.6.9-ha92aebf_0 conda-forge
traceback2: 1.4.0-py27_0 conda-forge
unittest2: 1.1.0-py_0 conda-forge
urllib3: 1.23-py27_1001 conda-forge
wheel: 0.32.3-py27_0 conda-forge
xz: 5.2.4-h470a237_1 conda-forge
zlib: 1.2.11-h470a237_3 conda-forge
Proceed ([y]/n)? y
Downloading and Extracting Packages
python-2.7.15 | 13.6 MB | ##################################### | 100%
pysam-0.14.1 | 7.2 MB | ##################################### | 100%
pb-dazzler-0.0.0 | 755 KB | ##################################### | 100%
cryptography-vectors | 30.5 MB | ##################################### | 100%
requests-2.20.1 | 83 KB | ##################################### | 100%
setuptools-40.6.2 | 622 KB | ##################################### | 100%
avro-python2-1.8.2 | 30 KB | ##################################### | 100%
python-sortedcontain | 25 KB | ##################################### | 100%
genomicconsensus-2.3 | 97 KB | ##################################### | 100%
python-consensuscore | 848 KB | ##################################### | 100%
enum34-1.1.6 | 56 KB | ##################################### | 100%
chardet-3.0.4 | 180 KB | ##################################### | 100%
pyopenssl-18.0.0 | 78 KB | ##################################### | 100%
linecache2-1.0.0 | 13 KB | ##################################### | 100%
urllib3-1.23 | 150 KB | ##################################### | 100%
pycparser-2.19 | 87 KB | ##################################### | 100%
python-consensuscore | 1.4 MB | ##################################### | 100%
pytz-2018.7 | 226 KB | ##################################### | 100%
cryptography-2.3.1 | 964 KB | ##################################### | 100%
python-edlib-1.2.3.p | 135 KB | ##################################### | 100%
pbcore-1.6.5 | 9.7 MB | ##################################### | 100%
pysocks-1.6.8 | 22 KB | ##################################### | 100%
cython-0.29 | 4.3 MB | ##################################### | 100%
future-0.17.0 | 708 KB | ##################################### | 100%
ipaddress-1.0.22 | 18 KB | ##################################### | 100%
pb-assembly-0.0.2 | 4 KB | ##################################### | 100%
six-1.11.0 | 20 KB | ##################################### | 100%
h5py-2.8.0 | 1.1 MB | ##################################### | 100%
asn1crypto-0.24.0 | 154 KB | ##################################### | 100%
cffi-1.11.5 | 388 KB | ##################################### | 100%
pb-falcon-0.2.4 | 716 KB | ##################################### | 100%
python-msgpack-0.5.6 | 282 KB | ##################################### | 100%
unittest2-1.1.0 | 68 KB | ##################################### | 100%
minimap2-2.14 | 2.0 MB | ##################################### | 100%
mkl-2018.0.3 | 198.7 MB | ##################################### | 100%
python-intervaltree- | 22 KB | ##################################### | 100%
pbcommand-1.1.1 | 193 KB | ##################################### | 100%
nim-falcon-0.0.0 | 271 KB | ##################################### | 100%
iso8601-0.1.12 | 9 KB | ##################################### | 100%
pbalign-0.3.1 | 76 KB | ##################################### | 100%
mummer4-4.0.0beta2 | 1.3 MB | ##################################### | 100%
mkl_random-1.0.2 | 1.0 MB | ##################################### | 100%
wheel-0.32.3 | 34 KB | ##################################### | 100%
intel-openmp-2019.1 | 885 KB | ##################################### | 100%
traceback2-1.4.0 | 28 KB | ##################################### | 100%
idna-2.7 | 131 KB | ##################################### | 100%
sqlite-3.25.3 | 1.6 MB | ##################################### | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: |
##############################################################################
# #
# PacBio(R) tools distributed via Bioconda are: pre-release versions, not #
# necessarily ISO compliant, intended for Research Use Only and not for use #
# in diagnostic procedures, intended only for command-line users, and #
# possibly newer than the currently available SMRT(R) Analysis builds. While #
# efforts have been made to ensure that releases on Bioconda live up to the #
# quality that PacBio strives for, we make no warranty regarding any #
# Bioconda release. #
# #
# As PacBio tools distributed via Bioconda are not covered by any service #
# level agreement or the like, please *do not* contact a PacBio Field #
# Applications Scientist or PacBio Customer Service for assistance with any #
# Bioconda release. We instead provide an issue tracker for you to report #
# issues to us at: #
# #
# https://github.com/PacificBiosciences/pbbioconda #
# #
# We make no warranty that any such issue will be addressed, #
# to any extent or within any time frame. #
# #
# BSD 3-Clause Clear License #
# #
# Please see https://github.com/PacificBiosciences/pbbioconda for #
# information on License, Copyright and Disclaimer #
# #
##############################################################################
/
##############################################################################
# #
# PacBio(R) tools distributed via Bioconda are: pre-release versions, not #
# necessarily ISO compliant, intended for Research Use Only and not for use #
# in diagnostic procedures, intended only for command-line users, and #
# possibly newer than the currently available SMRT(R) Analysis builds. While #
# efforts have been made to ensure that releases on Bioconda live up to the #
# quality that PacBio strives for, we make no warranty regarding any #
# Bioconda release. #
# #
# As PacBio tools distributed via Bioconda are not covered by any service #
# level agreement or the like, please *do not* contact a PacBio Field #
# Applications Scientist or PacBio Customer Service for assistance with any #
# Bioconda release. We instead provide an issue tracker for you to report #
# issues to us at: #
# #
# https://github.com/PacificBiosciences/pbbioconda #
# #
# We make no warranty that any such issue will be addressed, #
# to any extent or within any time frame. #
# #
# BSD 3-Clause Clear License #
# #
# Please see https://github.com/PacificBiosciences/pbbioconda for #
# information on License, Copyright and Disclaimer #
# #
##############################################################################
##############################################################################
# #
# PacBio(R) tools distributed via Bioconda are: pre-release versions, not #
# necessarily ISO compliant, intended for Research Use Only and not for use #
# in diagnostic procedures, intended only for command-line users, and #
# possibly newer than the currently available SMRT(R) Analysis builds. While #
# efforts have been made to ensure that releases on Bioconda live up to the #
# quality that PacBio strives for, we make no warranty regarding any #
# Bioconda release. #
# #
# As PacBio tools distributed via Bioconda are not covered by any service #
# level agreement or the like, please *do not* contact a PacBio Field #
# Applications Scientist or PacBio Customer Service for assistance with any #
# Bioconda release. We instead provide an issue tracker for you to report #
# issues to us at: #
# #
# https://github.com/PacificBiosciences/pbbioconda #
# #
# We make no warranty that any such issue will be addressed, #
# to any extent or within any time frame. #
# #
# BSD 3-Clause Clear License #
# #
# Please see https://github.com/PacificBiosciences/pbbioconda for #
# information on License, Copyright and Disclaimer #
# #
##############################################################################
##############################################################################
# #
# PacBio(R) tools distributed via Bioconda are: pre-release versions, not #
# necessarily ISO compliant, intended for Research Use Only and not for use #
# in diagnostic procedures, intended only for command-line users, and #
# possibly newer than the currently available SMRT(R) Analysis builds. While #
# efforts have been made to ensure that releases on Bioconda live up to the #
# quality that PacBio strives for, we make no warranty regarding any #
# Bioconda release. #
# #
# As PacBio tools distributed via Bioconda are not covered by any service #
# level agreement or the like, please *do not* contact a PacBio Field #
# Applications Scientist or PacBio Customer Service for assistance with any #
# Bioconda release. We instead provide an issue tracker for you to report #
# issues to us at: #
# #
# https://github.com/PacificBiosciences/pbbioconda #
# #
# We make no warranty that any such issue will be addressed, #
# to any extent or within any time frame. #
# #
# BSD 3-Clause Clear License #
# #
# Please see https://github.com/PacificBiosciences/pbbioconda for #
# information on License, Copyright and Disclaimer #
# #
##############################################################################
##############################################################################
# #
# PacBio(R) tools distributed via Bioconda are: pre-release versions, not #
# necessarily ISO compliant, intended for Research Use Only and not for use #
# in diagnostic procedures, intended only for command-line users, and #
# possibly newer than the currently available SMRT(R) Analysis builds. While #
# efforts have been made to ensure that releases on Bioconda live up to the #
# quality that PacBio strives for, we make no warranty regarding any #
# Bioconda release. #
# #
# As PacBio tools distributed via Bioconda are not covered by any service #
# level agreement or the like, please *do not* contact a PacBio Field #
# Applications Scientist or PacBio Customer Service for assistance with any #
# Bioconda release. We instead provide an issue tracker for you to report #
# issues to us at: #
# #
# https://github.com/PacificBiosciences/pbbioconda #
# #
# We make no warranty that any such issue will be addressed, #
# to any extent or within any time frame. #
# #
# BSD 3-Clause Clear License #
# #
# Please see https://github.com/PacificBiosciences/pbbioconda for #
# information on License, Copyright and Disclaimer #
# #
##############################################################################
done
(denovo_asm) ➜ Analysis_Results
