From e6b43371d012fb2f4cba6338ab98cab0b833e216 Mon Sep 17 00:00:00 2001 From: jfsanchezherrero Date: Tue, 19 Jul 2022 12:25:27 +0200 Subject: [PATCH] updates installation --- README.md | 33 ++- XICRA_pip/README.md | 23 +- XICRA_pip/VERSION | 2 +- .../XICRA/config/software/dependencies.csv | 2 +- XICRA_pip/XICRA/config/software/installer.sh | 8 + XICRA_pip/devel/conda/environment.yml | 265 ++++++++++-------- 6 files changed, 185 insertions(+), 148 deletions(-) diff --git a/README.md b/README.md index 8d1e458..298e143 100644 --- a/README.md +++ b/README.md @@ -37,24 +37,41 @@ Unfortunately, a couple of executables are not available neither as a `conda` or To create a new conda environment, install third party software, install XICRA and missing dependencies, do as follows: + +```sh +1) Get requirements file from XICRA git repo + ```sh -## clone repo -git clone https://github.com/HCGB-IGTP/XICRA.git +wget https://raw.githubusercontent.com/HCGB-IGTP/XICRA/master/XICRA_pip/devel/conda/environment.yml +``` -## move to folder -cd XICRA +2) Create environment and install required packages using conda: -## create conda environemt -conda env create -n XICRA -f XICRA_pip/devel/conda/requirements.txt +```sh +conda env create -n XICRA -f environment.yml +``` +3) Activate environment and install XICRA +```sh ## activate conda activate XICRA ## install latest python code pip install XICRA +``` +4) Install missing software: Unfortunately, a couple of executables are not available neither as a `conda` or `pip` packages. These packages are `miraligner` and `sRNAbench`. We have generated a `shell` script to retrieve and include within your `conda environment`. + +```sh ## install missing software -sh XICRA_pip/XICRA/config/software/installer.sh +wget https://raw.githubusercontent.com/HCGB-IGTP/XICRA/master/XICRA_pip/XICRA/config/software/installer.sh +sh installer.sh +``` + +To check everything is fine, try executing the `config` module: + +```sh +XICRA config ``` To check everything is fine, try executing the `config` module: @@ -94,7 +111,7 @@ See a brief example on how to install and run XICRA [here](https://github.com/HC MIT License -Copyright (c) 2020 HCGB-IGTP +Copyright (c) 2020-2022 HCGB-IGTP See additional details [here](XICRA_pip/LICENSE) diff --git a/XICRA_pip/README.md b/XICRA_pip/README.md index ba26291..4e99c3d 100644 --- a/XICRA_pip/README.md +++ b/XICRA_pip/README.md @@ -59,7 +59,8 @@ pip install XICRA ```sh ## install missing software -sh XICRA_pip/XICRA/config/software/installer.sh +wget https://raw.githubusercontent.com/HCGB-IGTP/XICRA/master/XICRA_pip/XICRA/config/software/installer.sh +sh installer.sh ``` To check everything is fine, try executing the `config` module: @@ -67,24 +68,6 @@ To check everything is fine, try executing the `config` module: XICRA config ``` -### Python environment - -If you are not using a `conda` environment as you might have previously installed all dependencies, we encourage you to create a python environment containing all python modules required for XICRA. See as an example this code: - -```sh -## create enviroment -python3 -m venv XICRA_env - -## activate it -source XICRA_env/bin/activate - -## install XICRA and dependencies -pip install XICRA - -## execute XICRA -XICRA -h -``` - ## Documentation See a full documentation, user guide and manual in [here](https://readthedocs.org/) @@ -121,7 +104,7 @@ See a brief example on how to install and run XICRA [here](https://github.com/HC MIT License -Copyright (c) 2020 HCGB-IGTP +Copyright (c) 2020-2022 HCGB-IGTP See additional details [here](XICRA_pip/LICENSE) diff --git a/XICRA_pip/VERSION b/XICRA_pip/VERSION index 347f583..9df886c 100644 --- a/XICRA_pip/VERSION +++ b/XICRA_pip/VERSION @@ -1 +1 @@ -1.4.1 +1.4.2 diff --git a/XICRA_pip/XICRA/config/software/dependencies.csv b/XICRA_pip/XICRA/config/software/dependencies.csv index 671b176..24284a1 100644 --- a/XICRA_pip/XICRA/config/software/dependencies.csv +++ b/XICRA_pip/XICRA/config/software/dependencies.csv @@ -15,6 +15,6 @@ optimir,,,na,optimir miraligner,,,na,miraligner.jar STAR,--version,([0-9\.]+).*,2.6.1,STAR featureCounts,-v,v([0-9\.]+).*,1.5.1,featureCounts -MINTmap,,,na,MINTmap.pl +MINTmap,,,na,MINTmap bedtools,-h,v([0-9\.]+).*,2.29.2,bedtools samtools,--version,samtools ([0-9\.]+).*,1.12,samtools diff --git a/XICRA_pip/XICRA/config/software/installer.sh b/XICRA_pip/XICRA/config/software/installer.sh index 0e11894..80b2191 100644 --- a/XICRA_pip/XICRA/config/software/installer.sh +++ b/XICRA_pip/XICRA/config/software/installer.sh @@ -37,6 +37,14 @@ echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++ " wget https://github.com/lpantano/seqbuster/raw/miraligner/modules/miraligner/miraligner.jar echo "" +echo "" +echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++ " +echo "## Downloading MINTmap" +echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++ " +wget -O MINTmap-v2.0-alpha.zip "https://cm.jefferson.edu/?smd_process_download=1&download_id=8044" +unzip MINTmap-v2.0-alpha.zip +pip install markupsafe==2.0.1 +pip install MINTmap-v2.0-alpha/dist/MINTmap-2.0a0-py3-none-any.whl echo "" ## mv files to conda enviornment folder diff --git a/XICRA_pip/devel/conda/environment.yml b/XICRA_pip/devel/conda/environment.yml index 4c57e11..9a4c937 100644 --- a/XICRA_pip/devel/conda/environment.yml +++ b/XICRA_pip/devel/conda/environment.yml @@ -1,140 +1,169 @@ name: XICRA channels: - - conda-forge - - r + - jfsanchezherrero - bioconda + - conda-forge - defaults dependencies: - _libgcc_mutex=0.1=main - - _r-mutex=1.0.0=anacondar_1 - - bedtools=2.30.0=hc088bd4_0 + - _openmp_mutex=4.5=1_gnu + - _r-mutex=1.0.1=anacondar_1 - binutils_impl_linux-64=2.33.1=he6710b0_7 - binutils_linux-64=2.33.1=h9595d00_15 - - biopython=1.78=py36h7b6447c_0 - - blas=1.0=mkl - - bowtie=1.2.0=py36_0 - - bowtie2=2.3.5.1=py36he513fc3_0 - - bwidget=1.9.11=1 - - bz2file=0.98=py36h06a4308_1 - - bzip2=1.0.8=h7b6447c_0 - - ca-certificates=2021.1.19=h06a4308_1 - - cairo=1.16.0=hf32fb01_1 - - certifi=2020.12.5=py36h06a4308_0 - - curl=7.69.1=hbc83047_0 - - cutadapt=1.18=py36h14c3975_1 - - fastq-join=1.3.1=hc9558a2_3 - - fastqc=0.11.9=hdfd78af_1 - - font-ttf-dejavu-sans-mono=2.37=h6964260_0 + - biopython=1.79=py37h5e8e339_0 + - bowtie2=2.2.5=py37h22450f8_8 + - bwidget=1.9.14=ha770c72_1 + - bz2file=0.98=py_0 + - bzip2=1.0.8=h7f98852_4 + - c-ares=1.17.1=h7f98852_1 + - ca-certificates=2022.6.15=ha878542_0 + - cairo=1.16.0=h18b612c_1001 + - certifi=2022.6.15=py37h89c1867_0 + - curl=7.76.1=h979ede3_1 - fontconfig=2.13.1=h6c09931_0 - - freetype=2.10.4=h5ab3b9f_0 - - fribidi=1.0.10=h7b6447c_0 + - freetype=2.10.4=h0708190_1 + - fribidi=1.0.10=h36c2ea0_0 - gcc_impl_linux-64=7.3.0=habb00fd_1 - gcc_linux-64=7.3.0=h553295d_15 + - gettext=0.19.8.1=h0b5b191_1005 - gfortran_impl_linux-64=7.3.0=hdf63c60_1 - gfortran_linux-64=7.3.0=h553295d_15 - - glib=2.67.4=h36276a3_1 - - graphite2=1.3.14=h23475e2_0 - - gsl=2.4=h14c3975_4 + - glib=2.68.3=h9c3ff4c_0 + - glib-tools=2.68.3=h9c3ff4c_0 + - graphite2=1.3.13=h58526e2_1001 + - gsl=2.4=h294904e_1006 - gxx_impl_linux-64=7.3.0=hdf63c60_1 - gxx_linux-64=7.3.0=h553295d_15 - - harfbuzz=2.8.0=h6f93f22_0 - - icu=58.2=he6710b0_3 - - intel-openmp=2020.2=254 - - jpeg=9b=h024ee3a_2 - - krb5=1.17.1=h173b8e3_0 + - harfbuzz=2.4.0=h37c48d4_1 + - htslib=1.12=h9093b5e_1 + - icu=58.2=hf484d3e_1000 + - jbig=2.1=h7f98852_2003 + - jpeg=9d=h36c2ea0_0 + - kernel-headers_linux-64=2.6.32=he073ed8_15 + - krb5=1.17.2=h926e7f8_0 - ld_impl_linux-64=2.33.1=h53a641e_7 - - libcurl=7.69.1=h20c2e04_0 - - libdeflate=1.0=h14c3975_1 - - libedit=3.1.20210216=h27cfd23_1 + - lerc=2.2.1=h9c3ff4c_0 + - libblas=3.9.0=8_openblas + - libcblas=3.9.0=8_openblas + - libcurl=7.76.1=hc4aaa36_1 + - libdeflate=1.7=h7f98852_5 + - libedit=3.1.20191231=he28a2e2_2 + - libev=4.33=h516909a_1 - libffi=3.3=he6710b0_2 - libgcc=7.2.0=h69d50b8_2 - - libgcc-ng=9.1.0=hdf63c60_0 - - libgfortran-ng=7.3.0=hdf63c60_0 - - libpng=1.6.37=hbc83047_0 - - libssh2=1.9.0=h1ba5d50_1 - - libstdcxx-ng=9.1.0=hdf63c60_0 - - libtiff=4.2.0=h85742a9_0 - - libuuid=1.0.3=h1bed415_2 - - libwebp-base=1.2.0=h27cfd23_0 - - libxcb=1.14=h7b6447c_0 - - libxml2=2.9.10=hb55368b_3 - - lz4-c=1.9.3=h2531618_0 - - make=4.2.1=h1bed415_1 - - mirtop=0.4.23=pyh864c0ab_1 - - mkl=2020.2=256 - - mkl-service=2.3.0=py36he8ac12f_0 - - mkl_fft=1.3.0=py36h54f3939_0 - - mkl_random=1.1.1=py36h0573a6f_0 + - libgcc-devel_linux-64=7.5.0=hda03d7c_19 + - libgcc-ng=9.3.0=h5101ec6_17 + - libgfortran-ng=7.5.0=h14aa051_19 + - libgfortran4=7.5.0=h14aa051_19 + - libglib=2.68.3=h3e27bee_0 + - libgomp=9.3.0=h5101ec6_17 + - libiconv=1.16=h516909a_0 + - liblapack=3.9.0=8_openblas + - libnghttp2=1.43.0=h812cca2_0 + - libopenblas=0.3.12=pthreads_hb3c22a3_1 + - libpng=1.6.37=h21135ba_2 + - libssh2=1.9.0=ha56f1ee_6 + - libstdcxx-devel_linux-64=7.5.0=hb016644_19 + - libstdcxx-ng=9.3.0=hd4cf53a_17 + - libtiff=4.3.0=hf544144_1 + - libuuid=1.0.3=h7f8727e_2 + - libwebp-base=1.2.0=h7f98852_2 + - libxcb=1.13=h7f98852_1003 + - libxml2=2.9.12=h03d6c58_0 + - lz4-c=1.9.3=h9c3ff4c_1 + - make=4.3=hd18ef5c_1 - ncurses=6.2=he6710b0_1 - - numpy=1.19.2=py36h54aff64_0 - - numpy-base=1.19.2=py36hfa32c7d_0 - - openjdk=8.0.152=h7b6447c_3 - - openssl=1.1.1k=h27cfd23_0 - - optimir=1.1=pyh3252c3a_0 - - pandas=1.1.3=py36he6710b0_0 - - pango=1.45.3=hd140c19_0 - - pcre=8.44=he6710b0_0 - - perl=5.26.2=h14c3975_0 - - perl-threaded=5.26.0=0 - - pigz=2.4=h84994c4_0 - - pip=21.0.1=py36h06a4308_0 - - pixman=0.40.0=h7b6447c_0 - - pybedtools=0.7.10=py36ha92aebf_3 - - pysam=0.15.3=py36hda2845c_1 - - python=3.6.13=hdb3f193_0 - - python-dateutil=2.8.1=pyhd3eb1b0_0 - - pytz=2021.1=pyhd3eb1b0_0 - - r-assertthat=0.2.1=r36h6115d3f_0 - - r-base=3.6.1=haffb61f_2 - - r-cli=1.1.0=r36h6115d3f_0 - - r-colorspace=1.4_1=r36h96ca727_0 - - r-crayon=1.3.4=r36h6115d3f_0 - - r-dichromat=2.0_0=r36h6115d3f_4 - - r-digest=0.6.18=r36h96ca727_0 - - r-fansi=0.4.0=r36h96ca727_0 - - r-getopt=1.20.3=r36h6115d3f_0 - - r-ggplot2=3.1.1=r36h6115d3f_0 - - r-glue=1.3.1=r36h96ca727_0 - - r-gtable=0.3.0=r36h6115d3f_0 - - r-labeling=0.3=r36h6115d3f_4 - - r-lattice=0.20_38=r36h96ca727_0 - - r-lazyeval=0.2.2=r36h96ca727_0 - - r-magrittr=1.5=r36h6115d3f_4 - - r-mass=7.3_51.3=r36h96ca727_0 - - r-matrix=1.2_17=r36h96ca727_0 - - r-mgcv=1.8_28=r36h96ca727_0 - - r-munsell=0.5.0=r36h6115d3f_0 - - r-nlme=3.1_139=r36ha65eedd_0 - - r-optparse=1.6.2=r36h6115d3f_0 - - r-pillar=1.3.1=r36h6115d3f_0 - - r-pkgconfig=2.0.2=r36h6115d3f_0 - - r-plyr=1.8.4=r36h29659fb_0 - - r-r6=2.4.0=r36h6115d3f_0 - - r-rcolorbrewer=1.1_2=r36h6115d3f_0 - - r-rcpp=1.0.1=r36h29659fb_0 - - r-reshape=0.8.8=r36h6115d3f_0 - - r-reshape2=1.4.3=r36h29659fb_0 - - r-rlang=0.3.4=r36h96ca727_0 - - r-scales=1.0.0=r36h29659fb_0 - - r-stringi=1.4.3=r36h29659fb_0 - - r-stringr=1.4.0=r36h6115d3f_0 - - r-tibble=2.1.1=r36h96ca727_0 - - r-utf8=1.1.4=r36h96ca727_0 - - r-viridislite=0.3.0=r36h6115d3f_0 - - r-withr=2.1.2=r36h6115d3f_0 + - openssl=1.1.1k=h7f98852_0 + - optimir=1.2=pyh5e36f6f_0 + - pango=1.42.4=h7062337_4 + - pcre=8.45=h9c3ff4c_0 + - perl=5.32.1=0_h7f98852_perl5 + - pigz=2.6=h27826a3_0 + - pip=21.0.1=py37h06a4308_0 + - pixman=0.38.0=h516909a_1003 + - pthread-stubs=0.4=h36c2ea0_1001 + - python=3.7.11=h12debd9_0 + - python_abi=3.7=2_cp37m + - r-assertthat=0.2.1=r35h6115d3f_1 + - r-backports=1.1.6=r35hcdcec82_1 + - r-base=3.5.3=h26b83e4_0 + - r-callr=3.4.3=r35h6115d3f_0 + - r-cli=2.0.2=r35h6115d3f_0 + - r-colorspace=1.4_1=r35hcdcec82_1 + - r-crayon=1.3.4=r35h6115d3f_1002 + - r-desc=1.2.0=r35h6115d3f_1002 + - r-digest=0.6.25=r35h0357c0b_1 + - r-dplyr=0.8.5=r35h0357c0b_0 + - r-ellipsis=0.3.0=r35hcdcec82_0 + - r-evaluate=0.14=r35h6115d3f_1 + - r-fansi=0.4.1=r35hcdcec82_0 + - r-farver=2.0.3=r35h0357c0b_0 + - r-getopt=1.20.3=r35_1 + - r-ggplot2=3.3.0=r35h6115d3f_0 + - r-glue=1.4.0=r35hcdcec82_0 + - r-gtable=0.3.0=r35h6115d3f_2 + - r-isoband=0.2.1=r35h0357c0b_0 + - r-labeling=0.3=r35h6115d3f_1002 + - r-lattice=0.20_41=r35hcdcec82_1 + - r-lifecycle=0.2.0=r35h6115d3f_0 + - r-magrittr=1.5=r35h6115d3f_1002 + - r-mass=7.3_51.6=r35hcdcec82_1 + - r-matrix=1.2_18=r35h7fa42b6_2 + - r-mgcv=1.8_31=r35h7fa42b6_0 + - r-munsell=0.5.0=r35h6115d3f_1002 + - r-nlme=3.1_147=r35h9bbef5b_0 + - r-optparse=1.6.6=r35h6115d3f_0 + - r-pillar=1.4.3=r35h6115d3f_0 + - r-pkgbuild=1.0.7=r35h6115d3f_0 + - r-pkgconfig=2.0.3=r35h6115d3f_0 + - r-pkgload=1.0.2=r35h0357c0b_1001 + - r-plogr=0.2.0=r35h6115d3f_1002 + - r-plyr=1.8.6=r35h0357c0b_0 + - r-praise=1.0.0=r35h6115d3f_1003 + - r-prettyunits=1.1.1=r35h6115d3f_0 + - r-processx=3.4.2=r35hcdcec82_0 + - r-ps=1.3.2=r35hcdcec82_0 + - r-purrr=0.3.4=r35hcdcec82_0 + - r-r6=2.4.1=r35h6115d3f_0 + - r-rcolorbrewer=1.1_2=r35h6115d3f_1002 + - r-rcpp=1.0.4.6=r35h0357c0b_0 + - r-reshape=0.8.8=r35hcdcec82_1 + - r-rlang=0.4.5=r35hcdcec82_2 + - r-rprojroot=1.3_2=r35h6115d3f_1002 + - r-rstudioapi=0.11=r35h6115d3f_0 + - r-scales=1.1.0=r35h6115d3f_0 + - r-stringi=1.4.3=r35h0357c0b_2 + - r-stringr=1.4.0=r35h6115d3f_1 + - r-testthat=2.3.2=r35h0357c0b_0 + - r-tibble=3.0.1=r35hcdcec82_0 + - r-tidyr=1.0.2=r35h0357c0b_0 + - r-tidyselect=1.0.0=r35h6115d3f_0 + - r-utf8=1.1.4=r35hcdcec82_1002 + - r-vctrs=0.2.4=r35hcdcec82_0 + - r-viridislite=0.3.0=r35h6115d3f_1002 + - r-withr=2.2.0=r35h6115d3f_0 + - r-xicra.stats=0.0.1=r35_0 + - r-zeallot=0.1.0=r35h6115d3f_1001 - readline=8.1=h27cfd23_0 - - samtools=1.7=1 - - setuptools=52.0.0=py36h06a4308_0 - - six=1.15.0=py36h06a4308_0 - - sqlite=3.35.2=hdfb4753_0 - - star=2.7.8a=0 - - subread=2.0.1=hed695b0_0 - - tbb=2020.3=hfd86e86_0 - - tk=8.6.10=hbc83047_0 - - tktable=2.10=h14c3975_0 - - viennarna=2.4.13=py36hdbcaa40_2 - - wheel=0.36.2=pyhd3eb1b0_0 - - xopen=0.7.3=py_0 + - samtools=1.12=h9aed4be_1 + - setuptools=58.0.4=py37h06a4308_0 + - sqlite=3.36.0=hc218d9a_0 + - star=2.7.9a=h9ee0642_0 + - sysroot_linux-64=2.12=he073ed8_15 + - tk=8.6.11=h1ccaba5_0 + - tktable=2.10=hb7b940f_3 + - wheel=0.37.0=pyhd3eb1b0_1 + - xorg-kbproto=1.0.7=h7f98852_1002 + - xorg-libice=1.0.10=h7f98852_0 + - xorg-libsm=1.2.2=h470a237_5 + - xorg-libx11=1.7.2=h7f98852_0 + - xorg-libxau=1.0.9=h7f98852_0 + - xorg-libxdmcp=1.1.3=h7f98852_0 + - xorg-libxext=1.3.4=h7f98852_1 + - xorg-libxrender=0.9.10=h7f98852_1003 + - xorg-renderproto=0.11.1=h7f98852_1002 + - xorg-xextproto=7.3.0=h7f98852_1002 + - xorg-xproto=7.0.31=h7f98852_1007 - xz=5.2.5=h7b6447c_0 - zlib=1.2.11=h7b6447c_3 - - zstd=1.4.5=h9ceee32_0 + - zstd=1.5.0=ha95c52a_0