search

wyang17 / SQuIRE

Software for Quantifying Interspersed Repeat Expression
Other
49 stars 30 forks source link

Unable to install squire, package dependency issue #87

Open tejas-j opened 1 year ago

tejas-j commented 1 year ago

I've been trying to install the tool but have the following error - from what I understand, the issue is due to bioconductor-genomeinfodbdata_1.1.0 package. Is there an alternate way to get the tool running?

Thank you!

(base) [user ~]$ mamba create -n squire -c bioconda squire

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (1.2.0) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

Looking for: ['squire']

bioconda/linux-64                                           Using cache
bioconda/noarch                                             Using cache
conda-forge/linux-64                                        Using cache
conda-forge/noarch                                          Using cache
pkgs/r/linux-64                                               No change
pkgs/main/linux-64                                            No change
pkgs/r/noarch                                                 No change
pkgs/main/noarch                                              No change
Transaction

  Prefix: /rsrch4/home/user/miniconda3/envs/squire

  Updating specs:

   - squire

  Package                                  Version  Build                    Channel                    Size
──────────────────────────────────────────────────────────────────────────────────────────────────────────────
  Install:
──────────────────────────────────────────────────────────────────────────────────────────────────────────────

  + _libgcc_mutex                              0.1  conda_forge              conda-forge/linux-64     Cached
  + _openmp_mutex                              4.5  2_gnu                    conda-forge/linux-64     Cached
  + _r-mutex                                 1.0.1  anacondar_1              conda-forge/noarch       Cached
  + alsa-lib                               1.2.3.2  h166bdaf_0               conda-forge/linux-64     Cached
  + bedtools                                2.25.0  he860b03_5               bioconda/linux-64        Cached
  + bioconductor-affy                       1.56.0  r3.4.1_0                 bioconda/linux-64        Cached
  + bioconductor-affyio                     1.50.0  r341h470a237_0           bioconda/linux-64        Cached
  + bioconductor-annotate                   1.58.0  r341_0                   bioconda/linux-64        Cached
  + bioconductor-annotationdbi              1.42.1  r341_0                   bioconda/linux-64        Cached
  + bioconductor-biobase                    2.40.0  r341h470a237_0           bioconda/linux-64        Cached
  + bioconductor-biocgenerics               0.26.0  r341_0                   bioconda/linux-64        Cached
  + bioconductor-biocinstaller              1.28.0  r341_1                   bioconda/linux-64        Cached
  + bioconductor-biocparallel               1.12.0  r341h219a75b_1           bioconda/linux-64        Cached
  + bioconductor-delayedarray                0.4.1  r3.4.1_0                 bioconda/linux-64        Cached
  + bioconductor-deseq2                     1.16.1  r3.4.1_3                 bioconda/linux-64        Cached
  + bioconductor-genefilter                 1.62.0  r341h26a2512_0           bioconda/linux-64        Cached
  + bioconductor-geneplotter                1.58.0  r341_0                   bioconda/linux-64        Cached
  + bioconductor-genomeinfodb               1.16.0  r341_0                   bioconda/linux-64        Cached
  + bioconductor-genomeinfodbdata            1.1.0  r341_0                   bioconda/linux-64        Cached
  + bioconductor-genomicranges              1.32.7  r341h470a237_0           bioconda/linux-64        Cached
  + bioconductor-iranges                   2.14.12  r341h470a237_0           bioconda/linux-64        Cached
  + bioconductor-limma                      3.36.5  r341h470a237_0           bioconda/linux-64        Cached
  + bioconductor-preprocesscore             1.42.0  r341h470a237_0           bioconda/linux-64        Cached
  + bioconductor-s4vectors                  0.18.3  r341h470a237_0           bioconda/linux-64        Cached
  + bioconductor-summarizedexperiment        1.8.0  r3.4.1_0                 bioconda/linux-64        Cached
  + bioconductor-tximport                    1.8.0  r341_0                   bioconda/linux-64        Cached
  + bioconductor-vsn                        3.46.0  r3.4.1_0                 bioconda/linux-64        Cached
  + bioconductor-xvector                    0.20.0  r341h470a237_0           bioconda/linux-64        Cached
  + bioconductor-zlibbioc                   1.26.0  r341h470a237_0           bioconda/linux-64        Cached
  + blas                                       1.1  openblas                 conda-forge/linux-64     Cached
  + bzip2                                    1.0.8  h7f98852_4               conda-forge/linux-64     Cached
  + ca-certificates                      2022.12.7  ha878542_0               conda-forge/linux-64     Cached
  + cairo                                   1.16.0  h18b612c_1001            conda-forge/linux-64     Cached
  + certifi                             2019.11.28  py27h8c360ce_1           conda-forge/linux-64     Cached
  + curl                                    7.61.0  h93b3f91_2               conda-forge/linux-64     Cached
  + expat                                    2.5.0  h27087fc_0               conda-forge/linux-64     Cached
  + fontconfig                              2.14.0  h8e229c2_0               conda-forge/linux-64     Cached
  + freetype                                2.10.4  h0708190_1               conda-forge/linux-64     Cached
  + gettext                                 0.21.1  h27087fc_0               conda-forge/linux-64     Cached
  + giflib                                   5.2.1  h36c2ea0_2               conda-forge/linux-64     Cached
  + glib                                    2.66.3  h58526e2_0               conda-forge/linux-64     Cached
  + graphite2                               1.3.13  h58526e2_1001            conda-forge/linux-64     Cached
  + gsl                                      2.2.1  blas_openblashddceaf2_6  conda-forge/linux-64     Cached
  + harfbuzz                                 2.4.0  h37c48d4_1               conda-forge/linux-64     Cached
  + icu                                       58.2  hf484d3e_1000            conda-forge/linux-64     Cached
  + igvtools                                2.3.93  0                        bioconda/linux-64        Cached
  + jpeg                                        9e  h166bdaf_2               conda-forge/linux-64     Cached
  + krb5                                    1.14.6  0                        conda-forge/linux-64     Cached
  + lcms2                                     2.12  hddcbb42_0               conda-forge/linux-64     Cached
  + lerc                                       3.0  h9c3ff4c_0               conda-forge/linux-64     Cached
  + libcurl                                 7.61.1  heec0ca6_0               pkgs/main/linux-64       Cached
  + libdeflate                                1.10  h7f98852_0               conda-forge/linux-64     Cached
  + libffi                                   3.2.1  he1b5a44_1007            conda-forge/linux-64     Cached
  + libgcc                                   7.2.0  h69d50b8_2               conda-forge/linux-64     Cached
  + libgcc-ng                               12.2.0  h65d4601_19              conda-forge/linux-64     Cached
  + libgfortran                              3.0.0  1                        conda-forge/linux-64     Cached
  + libgfortran-ng                           7.5.0  h14aa051_20              conda-forge/linux-64     Cached
  + libgfortran4                             7.5.0  h14aa051_20              conda-forge/linux-64     Cached
  + libglib                                 2.66.3  hbe7bbb4_0               conda-forge/linux-64     Cached
  + libgomp                                 12.2.0  h65d4601_19              conda-forge/linux-64     Cached
  + libiconv                                  1.17  h166bdaf_0               conda-forge/linux-64     Cached
  + libpng                                  1.6.37  h21135ba_2               conda-forge/linux-64     Cached
  + libssh2                                  1.8.0  h1ad7b7a_1003            conda-forge/linux-64     Cached
  + libstdcxx-ng                            12.2.0  h46fd767_19              conda-forge/linux-64     Cached
  + libtiff                                  4.3.0  h0fcbabc_4               conda-forge/linux-64     Cached
  + libuuid                                 2.32.1  h7f98852_1000            conda-forge/linux-64     Cached
  + libwebp-base                             1.2.4  h166bdaf_0               conda-forge/linux-64     Cached
  + libxcb                                    1.13  h7f98852_1004            conda-forge/linux-64     Cached
  + libxml2                                  2.9.9  h13577e0_2               conda-forge/linux-64     Cached
  + libzlib                                 1.2.11  h166bdaf_1014            conda-forge/linux-64     Cached
  + lz4-c                                    1.9.4  hcb278e6_0               conda-forge/linux-64     Cached
  + mysql-connector-c                        6.1.6  2                        bioconda/linux-64        Cached
  + ncurses                                    6.3  h27087fc_1               conda-forge/linux-64     Cached
  + openblas                                 0.3.3  h9ac9557_1001            conda-forge/linux-64     Cached
  + openjdk                                 11.0.8  hacce0ff_0               conda-forge/linux-64     Cached
  + openssl                                 1.0.2u  h516909a_0               conda-forge/linux-64     Cached
  + pango                                  1.40.14  he7ab937_1005            conda-forge/linux-64     Cached
  + pcre                                      8.45  h9c3ff4c_0               conda-forge/linux-64     Cached
  + pip                                     20.1.1  pyh9f0ad1d_0             conda-forge/noarch       Cached
  + pixman                                  0.38.0  h516909a_1003            conda-forge/linux-64     Cached
  + pthread-stubs                              0.4  h36c2ea0_1001            conda-forge/linux-64     Cached
  + pyfaidx                                  0.7.0  pyh5e36f6f_0             bioconda/noarch          Cached
  + python                                  2.7.15  h938d71a_1006            conda-forge/linux-64     Cached
  + python_abi                                 2.7  1_cp27mu                 conda-forge/linux-64     Cached
  + r-acepack                                1.4.1  r341h364d78e_2           conda-forge/linux-64     Cached
  + r-assertthat                             0.2.0  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-backports                              1.1.2  r341hc070d10_1           conda-forge/linux-64     Cached
  + r-base                                   3.4.1  h4fe35fd_8               conda-forge/linux-64     Cached
  + r-base64enc                              0.1_3  r341hc070d10_2           conda-forge/linux-64     Cached
  + r-bh                                  1.66.0_1  r341_1001                conda-forge/linux-64     Cached
  + r-bit                                   1.1_12  r341h470a237_2           conda-forge/linux-64     Cached
  + r-bit64                                  0.9_7  r341hc070d10_0           conda-forge/linux-64     Cached
  + r-bitops                                 1.0_6  r341hc070d10_2           conda-forge/linux-64     Cached
  + r-blob                                   1.1.1  r341_1                   conda-forge/linux-64     Cached
  + r-catools                             1.17.1.1  r341h9d2a408_2           conda-forge/linux-64     Cached
  + r-checkmate                              1.8.5  r341hc070d10_2           conda-forge/linux-64     Cached
  + r-cluster                              2.0.7_1  r341h364d78e_0           conda-forge/linux-64     Cached
  + r-colorspace                             1.3_2  r341hc070d10_2           conda-forge/linux-64     Cached
  + r-data.table                            1.11.6  r341hc070d10_0           bioconda/linux-64        Cached
  + r-dbi                                    1.0.0  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-digest                                0.6.18  r341hc070d10_0           conda-forge/linux-64     Cached
  + r-evaluate                                0.11  r341h6115d3f_0           conda-forge/linux-64     Cached
  + r-foreign                               0.8_71  r341hc070d10_2           conda-forge/linux-64     Cached
  + r-formatr                                  1.5  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-formula                                1.2_3  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-futile.logger                          1.4.3  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-futile.options                         1.0.1  r341h6115d3f_0           conda-forge/linux-64     Cached
  + r-gdata                                 2.18.0  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-getopt                                1.20.2  r341_1                   conda-forge/linux-64     Cached
  + r-ggplot2                                3.1.0  r341h6115d3f_0           conda-forge/linux-64     Cached
  + r-ggrepel                                0.8.0  r341h9d2a408_2           conda-forge/linux-64     Cached
  + r-glue                                   1.3.0  r341h470a237_2           conda-forge/linux-64     Cached
  + r-gplots                                 3.0.1  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-gridextra                                2.3  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-gtable                                 0.2.0  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-gtools                                 3.8.1  r341hc070d10_2           conda-forge/linux-64     Cached
  + r-hexbin                                1.27.2  r341h364d78e_2           conda-forge/linux-64     Cached
  + r-highr                                    0.7  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-hmisc                                  4.1_1  r341h364d78e_1           conda-forge/linux-64     Cached
  + r-htmltable                               1.12  r341h6115d3f_0           conda-forge/linux-64     Cached
  + r-htmltools                              0.3.6  r341hfc679d8_2           conda-forge/linux-64     Cached
  + r-htmlwidgets                              1.2  r341h6115d3f_0           conda-forge/linux-64     Cached
  + r-jsonlite                                 1.5  r341hc070d10_2           conda-forge/linux-64     Cached
  + r-kernsmooth                           2.23_15  r341h364d78e_2           conda-forge/linux-64     Cached
  + r-knitr                                   1.20  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-labeling                                 0.3  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-lambda.r                               1.2.3  r341h6115d3f_0           conda-forge/linux-64     Cached
  + r-lattice                              0.20_35  r341hc070d10_0           conda-forge/linux-64     Cached
  + r-latticeextra                          0.6_28  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-lazyeval                               0.2.1  r341hc070d10_2           conda-forge/linux-64     Cached
  + r-locfit                               1.5_9.1  r341h470a237_2           conda-forge/linux-64     Cached
  + r-magrittr                                 1.5  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-markdown                                 0.8  r341hc070d10_3           conda-forge/linux-64     Cached
  + r-mass                                  7.3_50  r341hc070d10_2           conda-forge/linux-64     Cached
  + r-matrix                                1.2_14  r341hc070d10_2           conda-forge/linux-64     Cached
  + r-matrixstats                           0.54.0  r341hc070d10_0           conda-forge/linux-64     Cached
  + r-memoise                                1.1.0  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-mgcv                                  1.8_24  r341hc070d10_2           conda-forge/linux-64     Cached
  + r-mime                                     0.5  r341hc070d10_2           conda-forge/linux-64     Cached
  + r-munsell                                0.5.0  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-nlme                                 3.1_137  r341h364d78e_0           conda-forge/linux-64     Cached
  + r-nnet                                  7.3_12  r341hc070d10_2           conda-forge/linux-64     Cached
  + r-pheatmap                              1.0.10  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-pkgconfig                              2.0.2  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-plogr                                  0.2.0  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-plyr                                   1.8.4  r341h9d2a408_2           conda-forge/linux-64     Cached
  + r-prettyunits                            1.0.2  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-r6                                     2.2.2  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-rcolorbrewer                           1.1_2  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-rcpp                                   1.0.0  r341h9d2a408_0           conda-forge/linux-64     Cached
  + r-rcpparmadillo                    0.9.100.5.0  r341h9d2a408_0           conda-forge/linux-64     Cached
  + r-rcurl                              1.95_4.11  r341hc070d10_3           conda-forge/linux-64     Cached
  + r-reshape2                               1.4.3  r341h9d2a408_2           conda-forge/linux-64     Cached
  + r-rjson                                 0.2.20  r341h9d2a408_0           conda-forge/linux-64     Cached
  + r-rlang                                0.3.0.1  r341h470a237_0           conda-forge/linux-64     Cached
  + r-rpart                                 4.1_13  r341hc070d10_2           conda-forge/linux-64     Cached
  + r-rsqlite                                2.1.1  r341h9d2a408_0           conda-forge/linux-64     Cached
  + r-rstudioapi                               0.7  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-scales                                 1.0.0  r341h9d2a408_1           conda-forge/linux-64     Cached
  + r-snow                                   0.4_3  r341h6115d3f_0           conda-forge/linux-64     Cached
  + r-stringi                                1.2.4  r341h9d2a408_1           conda-forge/linux-64     Cached
  + r-stringr                                1.3.1  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-survival                              2.42_6  r341hc070d10_1           conda-forge/linux-64     Cached
  + r-tibble                                 1.3.3  r3.4.1_0                 conda-forge/linux-64     Cached
  + r-viridis                                0.5.1  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-viridislite                            0.3.0  r341h6115d3f_1           conda-forge/linux-64     Cached
  + r-withr                                  2.1.2  r341h6115d3f_0           conda-forge/linux-64     Cached
  + r-xml                                3.98_1.16  r341hc070d10_0           conda-forge/linux-64     Cached
  + r-xtable                                 1.8_3  r341_1000                conda-forge/linux-64     Cached
  + r-yaml                                   2.2.0  r341hc070d10_1           conda-forge/linux-64     Cached
  + readline                                   7.0  hf8c457e_1001            conda-forge/linux-64     Cached
  + samtools                                   1.1  h20b1175_7               bioconda/linux-64        Cached
  + setuptools                              44.0.0  py27_0                   conda-forge/linux-64     Cached
  + six                                     1.16.0  pyh6c4a22f_0             conda-forge/noarch       Cached
  + sqlite                                  3.28.0  h8b20d00_0               conda-forge/linux-64     Cached
  + squire                                0.9.9.92  pyhdfd78af_1             bioconda/noarch          Cached
  + star                                    2.5.3a  0                        bioconda/linux-64        Cached
  + stringtie                                1.3.3  py27_3                   bioconda/linux-64        Cached
  + tk                                      8.6.12  h27826a3_0               conda-forge/linux-64     Cached
  + ucsc-bedgraphtobigwig                      377  h199ee4e_0               bioconda/linux-64        Cached
  + ucsc-genepredtobed                         377  h199ee4e_1               bioconda/linux-64        Cached
  + ucsc-genepredtogtf                         377  h199ee4e_1               bioconda/linux-64        Cached
  + ucsc-gtftogenepred                         377  h199ee4e_1               bioconda/linux-64        Cached
  + wget                                    1.19.5  h1ad7b7a_0               pkgs/main/linux-64       Cached
  + wheel                                   0.37.1  pyhd8ed1ab_0             conda-forge/noarch       Cached
  + xorg-fixesproto                            5.0  h7f98852_1002            conda-forge/linux-64     Cached
  + xorg-inputproto                          2.3.2  h7f98852_1002            conda-forge/linux-64     Cached
  + xorg-kbproto                             1.0.7  h7f98852_1002            conda-forge/linux-64     Cached
  + xorg-libice                             1.0.10  h7f98852_0               conda-forge/linux-64     Cached
  + xorg-libsm                               1.2.3  hd9c2040_1000            conda-forge/linux-64     Cached
  + xorg-libx11                              1.7.2  h7f98852_0               conda-forge/linux-64     Cached
  + xorg-libxau                              1.0.9  h7f98852_0               conda-forge/linux-64     Cached
  + xorg-libxdmcp                            1.1.3  h7f98852_0               conda-forge/linux-64     Cached
  + xorg-libxext                             1.3.4  h7f98852_1               conda-forge/linux-64     Cached
  + xorg-libxfixes                           5.0.3  h7f98852_1004            conda-forge/linux-64     Cached
  + xorg-libxi                              1.7.10  h7f98852_0               conda-forge/linux-64     Cached
  + xorg-libxrender                         0.9.10  h7f98852_1003            conda-forge/linux-64     Cached
  + xorg-libxt                               1.2.1  h7f98852_2               conda-forge/linux-64     Cached
  + xorg-libxtst                             1.2.3  h7f98852_1002            conda-forge/linux-64     Cached
  + xorg-recordproto                        1.14.2  h7f98852_1002            conda-forge/linux-64     Cached
  + xorg-renderproto                        0.11.1  h7f98852_1002            conda-forge/linux-64     Cached
  + xorg-xextproto                           7.3.0  h7f98852_1002            conda-forge/linux-64     Cached
  + xorg-xproto                             7.0.31  h7f98852_1007            conda-forge/linux-64     Cached
  + xz                                       5.2.6  h166bdaf_0               conda-forge/linux-64     Cached
  + zlib                                    1.2.11  h166bdaf_1014            conda-forge/linux-64     Cached
  + zstd                                     1.5.2  h8a70e8d_1               conda-forge/linux-64     Cached

  Summary:

  Install: 206 packages

  Total download: 0 B

──────────────────────────────────────────────────────────────────────────────────────────────────────────────

Confirm changes: [Y/n] y

Downloading and Extracting Packages

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
ERROR conda.core.link:_execute(740): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.1.0-r341_0'.
Rolling back transaction: done
post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.1.0-r341_0
location of failed script: /rsrch4/home/hema_bio-Malignan/trjammihal/miniconda3/envs/squire/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout: ERROR: post-link.sh was unable to download any of the following URLs with the md5sum e7fe0694dc065ebe8a7474d9b7afca63:
http://bioconductor.org/packages/3.7/data/annotation/src/contrib/GenomeInfoDbData_1.1.0.tar.gz
https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.1.0.tar.gz
https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.1.0_src_all.tar.gz

stderr: 
return code: 1

()

LinkError: post-link script failed for package bioconda::bioconductor-genomeinfodbdata-1.1.0-r341_0
location of failed script: /rsrch4/home/user/miniconda3/envs/squire/bin/.bioconductor-genomeinfodbdata-post-link.sh
==> script messages <==
<None>
==> script output <==
stdout: ERROR: post-link.sh was unable to download any of the following URLs with the md5sum e7fe0694dc065ebe8a7474d9b7afca63:
http://bioconductor.org/packages/3.7/data/annotation/src/contrib/GenomeInfoDbData_1.1.0.tar.gz
https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.1.0.tar.gz
https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.1.0_src_all.tar.gz

stderr: 
return code: 1

()
janoppelt commented 1 year ago

This is how I did it:

  1. Install Conda environment with all the dependencies (there might be some extra dependencies but I don't remeber which ones I added) and activate
mamba create --name squire --override-channels -c iuc -c bioconda -c conda-forge -c defaults -c r python=2.7.13 bioconductor-deseq2=1.16.1 r-base=3.4.1 r-pheatmap bioconductor-vsn bioconductor-biocparallel=1.12.0 star=2.5.3a bedtools=2.25.0 samtools=1.1 stringtie=1.3.3 igvtools=2.3.93 ucsc-genepredtobed ucsc-gtftogenepred ucsc-genepredtogtf ucsc-bedgraphtobigwig r-hexbin r-stringr r-ggrepel`

source activate squire
  1. Get SQuIRE from GitHub (I used my commit 868dd88 but I don't see why it shouldn't work with the latest original one)
git clone git@github.com:opplatek/SQuIRE.git
  1. Install SQuIRE with pip
cd SQuIRE/
pip install -e .
synnimeng commented 5 months ago

@opplatek Hi Oppelt! I also meet problems when installing SQuIRE. Could you please share your conda env as a .yaml file if possible? Thanks a lot!

janoppelt commented 2 months ago

@synnimeng here you go. There is a bunch of stuff you probably don't need, though. squire.txt