https://bioinformaticsonline.com/snippets/view/37907/installing-pb-assembly-on-linux? https://bioinformaticsonline.com/snippets/view/37907/installing-pb-assembly-on-linux Tue, 09 Oct 2018 10:24:43 -0500 https://bioinformaticsonline.com/snippets/view/37907/installing-pb-assembly-on-linux [jnarayan@hmem00 ~]$ module avail -------------------------------------------------------- /usr/share/Modules/modulefiles -------------------------------------------------------- Anaconda3/4.4.0 libreadline/6.3-foss-2016a Armadillo/2.4.4-goolf-1.4.10-Python-2.7.3 libreadline/6.3-foss-2016b arpack-ng/3.3.0-foss-2016a libreadline/7.0-GCCcore-6.4.0 ATLAS/3.8.4-gompi-1.1.0-no-OFED-LAPACK-3.4.0 libSM/1.2.2-foss-2016a Autoconf/2.69 libsndfile/1.0.28-foss-2016a Autoconf/2.69-foss-2016a libsndfile/1.0.28-GCCcore-6.4.0 Autoconf/2.69-foss-2016b LibTIFF/4.0.6-foss-2016a Autoconf/2.69-GCC-4.8.2 LibTIFF/4.0.6-foss-2016b Autoconf/2.69-GCCcore-6.4.0 LibTIFF/4.0.9-foss-2017b Autoconf/2.69-goolf-1.4.10 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xorg-macros/1.19.0-foss-2016a libGLU/9.0.0-foss-2016b xprop/1.2.2-foss-2016a libGLU/9.0.0-foss-2017b xproto/7.0.28-foss-2016a libICE/1.0.9-foss-2016a xtrans/1.3.5-foss-2016a libjpeg-turbo/1.4.2-foss-2016a XZ/5.2.2-foss-2016a libjpeg-turbo/1.5.0-foss-2016a XZ/5.2.2-foss-2016b libjpeg-turbo/1.5.0-foss-2016b XZ/5.2.2-GCCcore-5.4.0 libjpeg-turbo/1.5.2-GCCcore-6.4.0 XZ/5.2.3-GCCcore-6.4.0 libpciaccess/0.13.4-foss-2016a zlib/1.2.11 libpng/1.6.21-foss-2016a zlib/1.2.11-GCCcore-6.4.0 libpng/1.6.23-foss-2016a zlib/1.2.5-goolf-1.4.10 libpng/1.6.23-foss-2016b zlib/1.2.7-goalf-1.1.0-no-OFED libpng/1.6.24-foss-2016a zlib/1.2.7-goolf-1.4.10 libpng/1.6.24-foss-2016b zlib/1.2.8 libpng/1.6.2-goolf-1.4.10 zlib/1.2.8-foss-2016a libpng/1.6.32-GCCcore-6.4.0 zlib/1.2.8-foss-2016b libpng/1.6.6-goolf-1.4.10 zlib/1.2.8-GCCcore-4.9.3 libpthread-stubs/0.3-foss-2016a zlib/1.2.8-GCCcore-5.4.0 libreadline/6.2-goalf-1.1.0-no-OFED zlib/1.2.8-goolf-1.4.10 libreadline/6.2-goolf-1.4.10 ----------------------------------------------- /opt/cecisw/arch/easybuild//default//modules/all ----------------------------------------------- binutils/2.27-GCCcore-6.3.0 GCC/6.3.0-2.27 hwloc/1.11.5-GCC-6.3.0-2.27 zlib/1.2.11-GCCcore-6.3.0 Bison/3.0.4-GCCcore-6.3.0 GCCcore/6.3.0 M4/1.4.18-GCCcore-6.3.0 flex/2.6.3-GCCcore-6.3.0 help2man/1.47.4-GCCcore-6.3.0 numactl/2.0.11-GCC-6.3.0-2.27 [jnarayan@hmem00 ~]$ module load Anaconda3/4.4.0 [jnarayan@hmem00 ~]$ conda config --add channels defaults [jnarayan@hmem00 ~]$ conda config --add channels bioconda [jnarayan@hmem00 ~]$ conda config --add channels conda-forge [jnarayan@hmem00 ~]$ conda create -n denovo_asm [jnarayan@hmem00 ~]$ source activate denovo_asm (denovo_asm) [jnarayan@hmem00 ~]$ conda install -c bioconda pb-assembly Fetching package metadata ........... Solving package specifications: PackageNotFoundError: Dependencies missing in current linux-64 channels: - pb-assembly -> genomicconsensus -> python-consensuscore >=1.1.1 -> libstdcxx-ng >=4.9 - pb-assembly -> pb-dazzler -> libgcc-ng >=4.9 - pb-assembly -> pb-falcon >=0.2.0 -> python-msgpack - pb-assembly -> mummer4 -> perl 5.22.0* Close matches found; did you mean one of these? libgcc-ng: libgcc perl: perl-b, petl, pepr (and similarly for the other packages) (denovo_asm) [jnarayan@hmem00 ~]$ conda list # packages in environment at /home/unamur/URBE/jnarayan/.conda/envs/denovo_asm: # (denovo_asm) [jnarayan@hmem00 ~]$ conda config --add channels defaults Warning: 'defaults' already in 'channels' list, moving to the top (denovo_asm) [jnarayan@hmem00 ~]$ conda config --add channels bioconda (denovo_asm) [jnarayan@hmem00 ~]$ conda config --add channels conda-forge (denovo_asm) [jnarayan@hmem00 ~]$ conda install bwa Fetching package metadata ............. Solving package specifications: . Package plan for installation in environment /home/unamur/URBE/jnarayan/.conda/envs/denovo_asm: The following NEW packages will be INSTALLED: bwa: 0.7.17-ha92aebf_3 bioconda libgcc-ng: 7.2.0-hdf63c60_3 conda-forge perl: 5.26.2-h470a237_0 conda-forge zlib: 1.2.11-h470a237_3 conda-forge Proceed ([y]/n)? y libgcc-ng-7.2. 100% |################################| Time: 0:00:01 5.16 MB/s perl-5.26.2-h4 100% |################################| Time: 0:00:00 17.85 MB/s zlib-1.2.11-h4 100% |################################| Time: 0:00:00 6.23 MB/s bwa-0.7.17-ha9 100% |################################| Time: 0:00:00 23.66 MB/s (denovo_asm) [jnarayan@hmem00 ~]$ conda list # packages in environment at /home/unamur/URBE/jnarayan/.conda/envs/denovo_asm: # bwa 0.7.17 ha92aebf_3 bioconda libgcc-ng 7.2.0 hdf63c60_3 conda-forge perl 5.26.2 h470a237_0 conda-forge zlib 1.2.11 h470a237_3 conda-forge (denovo_asm) [jnarayan@hmem00 ~]$ conda install samtools Fetching package metadata ............. Solving package specifications: . Package plan for installation in environment /home/unamur/URBE/jnarayan/.conda/envs/denovo_asm: The following NEW packages will be INSTALLED: bzip2: 1.0.6-h470a237_2 conda-forge ca-certificates: 2018.8.24-ha4d7672_0 conda-forge curl: 7.61.1-h74213dd_2 conda-forge krb5: 1.16.1-hbb41f41_0 conda-forge libcurl: 7.61.1-hbdb9355_2 conda-forge libdeflate: 1.0-h470a237_0 bioconda libedit: 3.1.20170329-haf1bffa_1 conda-forge libssh2: 1.8.0-h5b517e9_2 conda-forge libstdcxx-ng: 7.2.0-hdf63c60_3 conda-forge ncurses: 6.1-hfc679d8_1 conda-forge openssl: 1.0.2p-h470a237_0 conda-forge samtools: 1.9-h8ee4bcc_1 bioconda tk: 8.6.8-ha92aebf_0 conda-forge xz: 5.2.4-h470a237_1 conda-forge Proceed ([y]/n)? y ca-certificate 100% |################################| Time: 0:00:00 496.03 kB/s libstdcxx-ng-7 100% |################################| Time: 0:00:00 3.08 MB/s bzip2-1.0.6-h4 100% |################################| Time: 0:00:00 22.55 MB/s libdeflate-1.0 100% |################################| Time: 0:00:00 2.98 MB/s ncurses-6.1-hf 100% |################################| Time: 0:00:00 19.67 MB/s openssl-1.0.2p 100% |################################| Time: 0:00:00 16.63 MB/s xz-5.2.4-h470a 100% |################################| Time: 0:00:00 13.07 MB/s libedit-3.1.20 100% |################################| Time: 0:00:00 8.84 MB/s libssh2-1.8.0- 100% |################################| Time: 0:00:00 11.11 MB/s tk-8.6.8-ha92a 100% |################################| Time: 0:00:00 22.37 MB/s krb5-1.16.1-hb 100% |################################| Time: 0:00:00 20.43 MB/s libcurl-7.61.1 100% |################################| Time: 0:00:00 15.26 MB/s curl-7.61.1-h7 100% |################################| Time: 0:00:00 7.61 MB/s samtools-1.9-h 100% |################################| Time: 0:00:00 15.03 MB/s (denovo_asm) [jnarayan@hmem00 ~]$ conda install -c bioconda pb-assembly Fetching package metadata ............. Solving package specifications: . Package plan for installation in environment /home/unamur/URBE/jnarayan/.conda/envs/denovo_asm: The following NEW packages will be INSTALLED: asn1crypto: 0.24.0-py27_1003 conda-forge avro: 1.8.0-py27_0 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 certifi: 2018.8.24-py27_1001 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 cython: 0.28.5-py27hfc679d8_0 conda-forge decorator: 4.3.0-py_0 conda-forge enum34: 1.1.6-py27_1001 conda-forge future: 0.16.0-py27_1002 conda-forge genomicconsensus: 2.3.2-py27_1 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 ipaddress: 1.0.22-py_1 conda-forge iso8601: 0.1.12-py_1 conda-forge libffi: 3.2.1-hfc679d8_5 conda-forge libgcc: 7.2.0-h69d50b8_2 conda-forge libgfortran: 3.0.0-1 conda-forge linecache2: 1.0.0-py_1 conda-forge minimap2: 2.12-ha92aebf_0 bioconda mkl: 2017.0.3-0 mummer4: 4.0.0beta2-pl526hfc679d8_3 bioconda networkx: 2.2-py_1 conda-forge nim-falcon: 0.0.0-0 bioconda numpy: 1.13.1-py27_0 pb-assembly: 0.0.1-py27_0 bioconda pb-dazzler: 0.0.0-h470a237_0 bioconda pb-falcon: 0.2.4-py27ha92aebf_0 bioconda pbalign: 0.3.1-py27_0 bioconda pbbam: 0.18.0-h1310cd9_1 bioconda pbcommand: 1.1.1-py27h24bf2e0_1 bioconda pbcore: 1.5.1-py27_1 bioconda 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_1 conda-forge python-consensuscore: 1.1.1-py27h02d93b8_1 bioconda python-consensuscore2: 3.1.0-py27_1 bioconda python-edlib: 1.2.3-py27h470a237_1 bioconda python-intervaltree: 2.1.0-py_0 bioconda python-msgpack: 0.5.6-py27h470a237_0 bioconda python-sortedcontainers: 2.0.4-py_0 bioconda pytz: 2018.5-py_0 conda-forge readline: 7.0-haf1bffa_1 conda-forge requests: 2.19.1-py27_1 conda-forge setuptools: 40.4.3-py27_0 conda-forge six: 1.11.0-py27_1001 conda-forge sqlite: 3.25.2-hb1c47c0_0 conda-forge traceback2: 1.4.0-py27_0 conda-forge unittest2: 1.1.0-py_0 conda-forge urllib3: 1.23-py27_1 conda-forge wheel: 0.32.1-py27_0 conda-forge Proceed ([y]/n)? y blas-1.0-mkl.t 100% |################################################################################################| Time: 0:00:00 794.99 kB/s libgfortran-3. 100% |################################################################################################| Time: 0:00:00 649.90 kB/s mkl-2017.0.3-0 100% |################################################################################################| Time: 0:00:05 24.66 MB/s nim-falcon-0.0 100% |################################################################################################| Time: 0:00:00 567.36 kB/s libffi-3.2.1-h 100% |################################################################################################| Time: 0:00:00 3.77 MB/s libgcc-7.2.0-h 100% |################################################################################################| Time: 0:00:00 2.60 MB/s pb-dazzler-0.0 100% |################################################################################################| Time: 0:00:00 3.76 MB/s bedtools-2.27. 100% |################################################################################################| Time: 0:00:00 7.25 MB/s hdf5-1.10.2-hc 100% |################################################################################################| Time: 0:00:00 11.66 MB/s minimap2-2.12- 100% |################################################################################################| Time: 0:00:00 12.76 MB/s mummer4-4.0.0b 100% |################################################################################################| Time: 0:00:00 23.60 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0:00:00 22.39 MB/s cryptography-v 100% |################################################################################################| Time: 0:00:01 22.15 MB/s cython-0.28.5- 100% |################################################################################################| Time: 0:00:00 23.39 MB/s decorator-4.3. 100% |################################################################################################| Time: 0:00:00 11.02 MB/s enum34-1.1.6-p 100% |################################################################################################| Time: 0:00:00 19.87 MB/s future-0.16.0- 100% |################################################################################################| Time: 0:00:00 23.69 MB/s idna-2.7-py27_ 100% |################################################################################################| Time: 0:00:00 21.70 MB/s ipaddress-1.0. 100% |################################################################################################| Time: 0:00:00 13.24 MB/s iso8601-0.1.12 100% |################################################################################################| Time: 0:00:00 10.62 MB/s linecache2-1.0 100% |################################################################################################| Time: 0:00:00 12.07 MB/s numpy-1.13.1-p 100% |################################################################################################| Time: 0:00:00 24.33 MB/s pycparser-2.19 100% |################################################################################################| Time: 0:00:00 18.60 MB/s pysocks-1.6.8- 100% |################################################################################################| Time: 0:00:00 7.09 MB/s python-edlib-1 100% |################################################################################################| Time: 0:00:00 21.74 MB/s python-msgpack 100% |################################################################################################| Time: 0:00:00 22.59 MB/s python-sortedc 100% |################################################################################################| Time: 0:00:00 13.18 MB/s pytz-2018.5-py 100% |################################################################################################| Time: 0:00:00 22.15 MB/s six-1.11.0-py2 100% |################################################################################################| Time: 0:00:00 14.04 MB/s bcftools-1.9-h 100% |################################################################################################| Time: 0:00:00 22.94 MB/s cffi-1.11.5-py 100% |################################################################################################| Time: 0:00:00 22.36 MB/s htslib-1.7-0.t 100% |################################################################################################| Time: 0:00:00 23.20 MB/s python-consens 100% |################################################################################################| Time: 0:00:00 21.20 MB/s python-consens 100% |################################################################################################| Time: 0:00:00 23.70 MB/s python-interva 100% |################################################################################################| Time: 0:00:00 6.24 MB/s setuptools-40. 100% |################################################################################################| Time: 0:00:00 23.17 MB/s traceback2-1.4 100% |################################################################################################| Time: 0:00:00 15.98 MB/s cryptography-2 100% |################################################################################################| Time: 0:00:00 21.84 MB/s networkx-2.2-p 100% |################################################################################################| Time: 0:00:00 22.74 MB/s pbbam-0.18.0-h 100% |################################################################################################| Time: 0:00:00 22.97 MB/s pysam-0.14.1-p 100% |################################################################################################| Time: 0:00:00 21.39 MB/s unittest2-1.1. 100% |################################################################################################| Time: 0:00:00 19.96 MB/s wheel-0.32.1-p 100% |################################################################################################| Time: 0:00:00 16.93 MB/s blasr_libcpp-5 100% |################################################################################################| Time: 0:00:00 20.38 MB/s h5py-2.8.0-py2 100% |################################################################################################| Time: 0:00:00 21.87 MB/s pb-falcon-0.2. 100% |################################################################################################| Time: 0:00:00 23.30 MB/s pip-18.1-py27_ 100% |################################################################################################| Time: 0:00:00 23.75 MB/s pyopenssl-18.0 100% |################################################################################################| Time: 0:00:00 21.84 MB/s blasr-5.3.2-ha 100% |################################################################################################| Time: 0:00:00 22.51 MB/s pbcore-1.5.1-p 100% |################################################################################################| Time: 0:00:00 21.71 MB/s urllib3-1.23-p 100% |################################################################################################| Time: 0:00:00 22.18 MB/s requests-2.19. 100% |################################################################################################| Time: 0:00:00 21.90 MB/s pbcommand-1.1. 100% |################################################################################################| Time: 0:00:00 21.83 MB/s genomicconsens 100% |################################################################################################| Time: 0:00:00 21.17 MB/s pbalign-0.3.1- 100% |################################################################################################| Time: 0:00:00 21.06 MB/s pb-assembly-0. 100% |################################################################################################| Time: 0:00:00 4.73 MB/s ############################################################################## # # # 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 # # # ############################################################################## (denovo_asm) [jnarayan@hmem00 ~]$ conda list # packages in environment at /home/unamur/URBE/jnarayan/.conda/envs/denovo_asm: # asn1crypto 0.24.0 py27_1003 conda-forge avro 1.8.0 py27_0 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 2018.8.24 ha4d7672_0 conda-forge certifi 2018.8.24 py27_1001 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 7.61.1 h74213dd_2 conda-forge cython 0.28.5 py27hfc679d8_0 conda-forge decorator 4.3.0 py_0 conda-forge enum34 1.1.6 py27_1001 conda-forge future 0.16.0 py27_1002 conda-forge genomicconsensus 2.3.2 py27_1 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 ipaddress 1.0.22 py_1 conda-forge iso8601 0.1.12 py_1 conda-forge krb5 1.16.1 hbb41f41_0 conda-forge libcurl 7.61.1 hbdb9355_2 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 libssh2 1.8.0 h5b517e9_2 conda-forge libstdcxx-ng 7.2.0 hdf63c60_3 conda-forge linecache2 1.0.0 py_1 conda-forge minimap2 2.12 ha92aebf_0 bioconda mkl 2017.0.3 0 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 1.13.1 py27_0 openssl 1.0.2p h470a237_0 conda-forge pb-assembly 0.0.1 py27_0 bioconda pb-dazzler 0.0.0 h470a237_0 bioconda pb-falcon 0.2.4 py27ha92aebf_0 bioconda pbalign 0.3.1 py27_0 bioconda pbbam 0.18.0 h1310cd9_1 bioconda pbcommand 1.1.1 py27h24bf2e0_1 bioconda pbcore 1.5.1 py27_1 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_1 conda-forge python-consensuscore 1.1.1 py27h02d93b8_1 bioconda python-consensuscore2 3.1.0 py27_1 bioconda python-edlib 1.2.3 py27h470a237_1 bioconda python-intervaltree 2.1.0 py_0 bioconda python-msgpack 0.5.6 py27h470a237_0 bioconda python-sortedcontainers 2.0.4 py_0 bioconda pytz 2018.5 py_0 conda-forge readline 7.0 haf1bffa_1 conda-forge requests 2.19.1 py27_1 conda-forge samtools 1.9 h8ee4bcc_1 bioconda setuptools 40.4.3 py27_0 conda-forge six 1.11.0 py27_1001 conda-forge sqlite 3.25.2 hb1c47c0_0 conda-forge tk 8.6.8 ha92aebf_0 conda-forge traceback2 1.4.0 py27_0 conda-forge unittest2 1.1.0 py_0 conda-forge urllib3 1.23 py27_1 conda-forge wheel 0.32.1 py27_0 conda-forge xz 5.2.4 h470a237_1 conda-forge zlib 1.2.11 h470a237_3 conda-forge (denovo_asm) [jnarayan@hmem00 ~]$ fc fc fc_emit_haplotigs.py fc_ovlp_stats fc_rr_hctg_track.exe fc_actg_coordinate fc_fasta2fasta fc_ovlp_to_graph fc_rr_hctg_track.py fcaps fc_fetch_reads fc-pattern fc_run fc-cache fc_filt_hp.py fc_phased_ovlp_to_graph.py fc_run1 fc_calc_cutoff fc_gen_gfa_v1 fc_phase.py fc_run.py fc-cat fc_get_read_ctg_map fc_phasing_readmap.py fc-scan fc_consensus fc_get_read_hctg_map.py fc_pr_ctg_track fc_scrub_names.pl fc_consensus.exe fc_graph_to_contig fc_primary_contig_index.pl fc_select_reads_from_bam.py fc_contig_annotate fc_graph_to_utgs fc-query fc_unzip_gen_gfa_v1.py fc_coords2hp.py fc-list fc_quiver.py fc_unzip.py fc_ctg_link_analysis fc-match fc_rr_ctg_track fc-validate fc_dedup_a_t]]> Jit