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zheminzhou / StrTrak

StrTrak: Strain Tracker for metagenomic data
GNU General Public License v3.0
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As for the installation of StrTrak #4

Open BurinkiWU opened 2 weeks ago

BurinkiWU commented 2 weeks ago

To whom it concerns:

I met some issues while installing the StrTrak, as the following shows: # Traceback (most recent call last): File "/home/wuzq-cdc/tools/StrTrak/./StrTrak", line 2, in import strBase, strPhylo, strProfile File "/home/wuzq-cdc/tools/StrTrak/strBase.py", line 1, in import os, gzip, click, glob, re, igraph ModuleNotFoundError: No module named 'igraph' # Actually, I have installed these packages in conda env. There are listed below: _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge alsa-lib 1.2.12 h4ab18f5_0 conda-forge arpack 3.9.1 nompi_h77f6705_101 conda-forge attr 2.5.1 h166bdaf_1 conda-forge aws-c-auth 0.7.22 h96bc93b_2 conda-forge aws-c-cal 0.6.14 h88a6e22_1 conda-forge aws-c-common 0.9.19 h4ab18f5_0 conda-forge aws-c-compression 0.2.18 h83b837d_6 conda-forge aws-c-event-stream 0.4.2 ha47c788_12 conda-forge aws-c-http 0.8.1 h29d6fba_17 conda-forge aws-c-io 0.14.8 h21d4f22_5 conda-forge aws-c-mqtt 0.10.4 h759edc4_4 conda-forge aws-c-s3 0.5.9 h594631b_3 conda-forge aws-c-sdkutils 0.1.16 h83b837d_2 conda-forge aws-checksums 0.1.18 h83b837d_6 conda-forge aws-crt-cpp 0.26.9 he3a8b3b_0 conda-forge aws-sdk-cpp 1.11.329 hba8bd5f_3 conda-forge bindash 2.3 hdcf5f25_2 bioconda biopython 1.83 py311h459d7ec_0 conda-forge bzip2 1.0.8 h5eee18b_6
c-ares 1.28.1 hd590300_0 conda-forge ca-certificates 2024.6.2 hbcca054_0 conda-forge cairo 1.18.0 h3faef2a_0 conda-forge click 8.1.7 unix_pyh707e725_0 conda-forge cramjam 2.8.3 py311h46250e7_0 conda-forge dbus 1.13.6 h5008d03_3 conda-forge emboss 6.6.0 h1617ff0_10 bioconda ete3 3.1.3 pyhd8ed1ab_0 conda-forge expat 2.6.2 h59595ed_0 conda-forge fastparquet 2024.5.0 py311h18e1886_0 conda-forge font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge font-ttf-inconsolata 3.000 h77eed37_0 conda-forge font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge font-ttf-ubuntu 0.83 h77eed37_2 conda-forge fontconfig 2.14.2 h14ed4e7_0 conda-forge fonts-conda-ecosystem 1 0 conda-forge fonts-conda-forge 1 0 conda-forge freetype 2.12.1 h267a509_2 conda-forge fsspec 2024.6.0 pyhff2d567_0 conda-forge gettext 0.22.5 h59595ed_2 conda-forge gettext-tools 0.22.5 h59595ed_2 conda-forge gflags 2.2.2 he1b5a44_1004 conda-forge giflib 5.2.2 hd590300_0 conda-forge glib 2.80.2 hf974151_0 conda-forge glib-tools 2.80.2 hb6ce0ca_0 conda-forge glog 0.7.1 hbabe93e_0 conda-forge glpk 5.0 h445213a_0 conda-forge gmp 6.3.0 h59595ed_1 conda-forge graphite2 1.3.13 h59595ed_1003 conda-forge gst-plugins-base 1.24.4 h9ad1361_0 conda-forge gstreamer 1.24.4 haf2f30d_0 conda-forge harfbuzz 8.5.0 hfac3d4d_0 conda-forge hmmer 3.4 hdbdd923_1 bioconda htslib 1.20 h5efdd21_1 bioconda icu 73.2 h59595ed_0 conda-forge igraph 0.10.12 hef0740d_1 conda-forge iqtree 2.3.4 hdcf5f25_2 bioconda k8 0.2.5 hdcf5f25_4 bioconda keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.21.2 h659d440_0 conda-forge lame 3.100 h166bdaf_1003 conda-forge ld_impl_linux-64 2.38 h1181459_1
lerc 4.0.0 h27087fc_0 conda-forge libabseil 20240116.2 cxx17_h59595ed_0 conda-forge libarrow 16.1.0 hcb6531f_6_cpu conda-forge libarrow-acero 16.1.0 hac33072_6_cpu conda-forge libarrow-dataset 16.1.0 hac33072_6_cpu conda-forge libarrow-substrait 16.1.0 h7e0c224_6_cpu conda-forge libasprintf 0.22.5 h661eb56_2 conda-forge libasprintf-devel 0.22.5 h661eb56_2 conda-forge libblas 3.9.0 22_linux64_openblas conda-forge libbrotlicommon 1.1.0 hd590300_1 conda-forge libbrotlidec 1.1.0 hd590300_1 conda-forge libbrotlienc 1.1.0 hd590300_1 conda-forge libcap 2.69 h0f662aa_0 conda-forge libcblas 3.9.0 22_linux64_openblas conda-forge libclang-cpp15 15.0.7 default_h127d8a8_5 conda-forge libclang13 18.1.7 default_h087397f_0 conda-forge libcrc32c 1.1.2 h9c3ff4c_0 conda-forge libcups 2.3.3 h4637d8d_4 conda-forge libcurl 8.8.0 hca28451_0 conda-forge libdeflate 1.20 hd590300_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 hd590300_2 conda-forge libevent 2.1.12 hf998b51_1 conda-forge libexpat 2.6.2 h59595ed_0 conda-forge libffi 3.4.4 h6a678d5_1
libflac 1.4.3 h59595ed_0 conda-forge libgcc-ng 13.2.0 h77fa898_11 conda-forge libgcrypt 1.10.3 hd590300_0 conda-forge libgd 2.3.3 h119a65a_9 conda-forge libgettextpo 0.22.5 h59595ed_2 conda-forge libgettextpo-devel 0.22.5 h59595ed_2 conda-forge libgfortran-ng 13.2.0 h69a702a_11 conda-forge libgfortran5 13.2.0 h3d2ce59_11 conda-forge libglib 2.80.2 hf974151_0 conda-forge libgomp 13.2.0 h77fa898_11 conda-forge libgoogle-cloud 2.24.0 h2736e30_0 conda-forge libgoogle-cloud-storage 2.24.0 h3d9a0c8_0 conda-forge libgpg-error 1.49 h4f305b6_0 conda-forge libgrpc 1.62.2 h15f2491_0 conda-forge libharu 2.4.4 h267a509_0 conda-forge libiconv 1.17 hd590300_2 conda-forge libjpeg-turbo 3.0.0 hd590300_1 conda-forge liblapack 3.9.0 22_linux64_openblas conda-forge libllvm14 14.0.6 hcd5def8_4 conda-forge libllvm15 15.0.7 hb3ce162_4 conda-forge libllvm18 18.1.7 hb77312f_0 conda-forge libnghttp2 1.58.0 h47da74e_1 conda-forge libnsl 2.0.1 hd590300_0 conda-forge libogg 1.3.4 h7f98852_1 conda-forge libopenblas 0.3.27 pthreads_h413a1c8_0 conda-forge libopus 1.3.1 h7f98852_1 conda-forge libparquet 16.1.0 h6a7eafb_6_cpu conda-forge libpng 1.6.43 h2797004_0 conda-forge libpq 16.3 ha72fbe1_0 conda-forge libprotobuf 4.25.3 h08a7969_0 conda-forge libre2-11 2023.09.01 h5a48ba9_2 conda-forge libsndfile 1.2.2 hc60ed4a_1 conda-forge libsqlite 3.45.2 h2797004_0 conda-forge libssh2 1.11.0 h0841786_0 conda-forge libstdcxx-ng 13.2.0 hc0a3c3a_11 conda-forge libsystemd0 255 h3516f8a_1 conda-forge libthrift 0.19.0 hb90f79a_1 conda-forge libtiff 4.6.0 h1dd3fc0_3 conda-forge libutf8proc 2.8.0 h166bdaf_0 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libvorbis 1.3.7 h9c3ff4c_0 conda-forge libwebp 1.4.0 h2c329e2_0 conda-forge libwebp-base 1.4.0 hd590300_0 conda-forge libxcb 1.15 h0b41bf4_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libxkbcommon 1.7.0 h662e7e4_0 conda-forge libxml2 2.12.7 hc051c1a_1 conda-forge libxslt 1.1.39 h76b75d6_0 conda-forge libzlib 1.2.13 h4ab18f5_6 conda-forge llvmlite 0.42.0 py311ha6695c7_1 conda-forge lxml 5.2.2 py311hc0a218f_0 conda-forge lz4-c 1.9.4 hcb278e6_0 conda-forge minimap2 2.28 he4a0461_1 bioconda mpg123 1.32.6 h59595ed_0 conda-forge mysql-common 8.3.0 hf1915f5_4 conda-forge mysql-libs 8.3.0 hca2cd23_4 conda-forge ncurses 6.5 h59595ed_0 conda-forge nspr 4.35 h27087fc_0 conda-forge nss 3.98 h1d7d5a4_0 conda-forge numba 0.59.1 py311h96b013e_0 conda-forge numpy 1.26.4 py311h64a7726_0 conda-forge openssl 3.3.1 h4ab18f5_0 conda-forge orc 2.0.1 h17fec99_1 conda-forge packaging 24.1 pyhd8ed1ab_0 conda-forge pandas 2.2.2 py311h14de704_1 conda-forge pcre2 10.43 hcad00b1_0 conda-forge pip 24.0 py311h06a4308_0
pixman 0.43.2 h59595ed_0 conda-forge ply 3.11 pyhd8ed1ab_2 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge pulseaudio-client 17.0 hb77b528_0 conda-forge pyarrow 16.1.0 py311h781c19f_1 conda-forge pyarrow-core 16.1.0 py311h8e2c35d_1_cpu conda-forge pyqt 5.15.9 py311hf0fb5b6_5 conda-forge pyqt5-sip 12.12.2 py311hb755f60_5 conda-forge python 3.11.8 hab00c5b_0_cpython conda-forge python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge python_abi 3.11 4_cp311 conda-forge pytz 2024.1 pyhd8ed1ab_0 conda-forge qt-main 5.15.8 hc9dc06e_21 conda-forge re2 2023.09.01 h7f4b329_2 conda-forge readline 8.2 h5eee18b_0
s2n 1.4.15 he19d79f_0 conda-forge samtools 1.20 h50ea8bc_0 bioconda scipy 1.13.1 py311h517d4fd_0 conda-forge setuptools 69.5.1 py311h06a4308_0
sip 6.7.12 py311hb755f60_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge snappy 1.2.0 hdb0a2a9_1 conda-forge sqlite 3.45.2 h2c6b66d_0 conda-forge tk 8.6.13 noxft_h4845f30_101 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge tomli 2.0.1 pyhd8ed1ab_0 conda-forge tzdata 2024a h04d1e81_0
wheel 0.43.0 py311h06a4308_0
xcb-util 0.4.0 hd590300_1 conda-forge xcb-util-image 0.4.0 h8ee46fc_1 conda-forge xcb-util-keysyms 0.4.0 h8ee46fc_1 conda-forge xcb-util-renderutil 0.3.9 hd590300_1 conda-forge xcb-util-wm 0.4.1 h8ee46fc_1 conda-forge xkeyboard-config 2.42 h4ab18f5_0 conda-forge xorg-kbproto 1.0.7 h7f98852_1002 conda-forge xorg-libice 1.1.1 hd590300_0 conda-forge xorg-libsm 1.2.4 h7391055_0 conda-forge xorg-libx11 1.8.9 h8ee46fc_0 conda-forge xorg-libxau 1.0.11 hd590300_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xorg-libxext 1.3.4 h0b41bf4_2 conda-forge xorg-libxrender 0.9.11 hd590300_0 conda-forge xorg-renderproto 0.11.1 h7f98852_1002 conda-forge xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge xorg-xf86vidmodeproto 2.3.1 h7f98852_1002 conda-forge xorg-xproto 7.0.31 h7f98852_1007 conda-forge xz 5.4.6 h5eee18b_1
zlib 1.2.13 h4ab18f5_6 conda-forge zstd 1.5.6 ha6fb4c9_0 conda-forge

Best regards, Bruce

BurinkiWU commented 2 weeks ago

I have fixed this problem.

For your information: When you install the requirement package of igraph, it is better to use the following command - "pip install python_igraph" under the environment of "strtrak".