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wyang17 / SQuIRE

Software for Quantifying Interspersed Repeat Expression
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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
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  + bioconductor-affy                       1.56.0  r3.4.1_0                 bioconda/linux-64        Cached
  + bioconductor-affyio                     1.50.0  r341h470a237_0           bioconda/linux-64        Cached
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  + bioconductor-geneplotter                1.58.0  r341_0                   bioconda/linux-64        Cached
  + bioconductor-genomeinfodb               1.16.0  r341_0                   bioconda/linux-64        Cached
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  + libgfortran                              3.0.0  1                        conda-forge/linux-64     Cached
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  + python                                  2.7.15  h938d71a_1006            conda-forge/linux-64     Cached
  + python_abi                                 2.7  1_cp27mu                 conda-forge/linux-64     Cached
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  + 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
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  + r-labeling                                 0.3  r341h6115d3f_1           conda-forge/linux-64     Cached
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  + 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
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  + 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
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  + r-rcpparmadillo                    0.9.100.5.0  r341h9d2a408_0           conda-forge/linux-64     Cached
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  + r-rpart                                 4.1_13  r341hc070d10_2           conda-forge/linux-64     Cached
  + r-rsqlite                                2.1.1  r341h9d2a408_0           conda-forge/linux-64     Cached
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  + r-scales                                 1.0.0  r341h9d2a408_1           conda-forge/linux-64     Cached
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  + r-stringi                                1.2.4  r341h9d2a408_1           conda-forge/linux-64     Cached
  + r-stringr                                1.3.1  r341h6115d3f_1           conda-forge/linux-64     Cached
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  + 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

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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 3 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 1 week ago

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