https://bioinformaticsonline.com/snippets/view/38290/setting-up-falconunzip-conda-environments-for-genome-assembly? https://bioinformaticsonline.com/snippets/view/38290/setting-up-falconunzip-conda-environments-for-genome-assembly Fri, 23 Nov 2018 12:01:02 -0600 https://bioinformaticsonline.com/snippets/view/38290/setting-up-falconunzip-conda-environments-for-genome-assembly ➜ 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]]> Jit