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--- phylogeny_protocol5 [2022/02/07 14:12] – created 134.190.232.106
+++ phylogeny_protocol5 [2022/02/08 14:02] (current) – 134.190.232.106
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-It is often annoying to install
+**How to build a YAML file thereby setting up Conda environment?**
+"//Users should be able to focus in their science, not in installing and managing software, so make it easy to them is fundamental.// " - Advice for Bioinformaticians.
+**Background**
+It is often annoying to set up installation dependencies(i.e., folder directory, hardcoded $PATH, and versions),especially when software developer does not follow good programming practices, such as avoiding hardcoded paths to file or script.
+To make the tools/pipelines more user friendly and reproducible, it is necessary make the installing process concise and straightforward thereby the most debugging efforts can be avoided.
+To speed up the installation process, developers usually prepare a conda environment definition file with all the dependencies listed, or/and a dockerfile to build an image (ideally both). Then install it into the conda environment or make it somehow findable by the $PATH system variable.
+**Build Yaml file**
+Taking the software pipeline PhyloToL as an example (Ceron-Romeroet.al.,2019), which requires the following dependencies.
+  - • Biopython (https://biopython.org/)
+  - • DendroPy (https://dendropy.org/)
+  - • P4 (http://p4.nhm.ac.uk/)
+  - • Bioperl (https://bioperl.org/)
+  - • MAFFT (v7; https://mafft.cbrc.jp/alignment/software/)
+  - • USEARCH (any version; https://www.drive5.com/usearch/)
+  - • Guidance (v2.02; http://guidance.tau.ac.il/overview.html)
+  - • trimAl (v1.3; http://trimal.cgenomics.org/)
+  - • RAxML (v8; https://cme.h-its.org/exelixis/web/software/raxml/index.html)
+. First set up a Conda environment file name.
+<code>
+conda create -n PhyloToL python=3.6
+# Since most scripts in PhyloToL are Python3, so we first start with installing the python dependencies.
+# Since macOS, linux can have different software distributions, here since I tested it on Perun which run on Ubuntu linux system, so all the software packages are Linux compatible not for MacOS.
+</code>
+. It is easy to use conda to install Biopython, DendroPy, Bioperl, MAFFT, Guidance, trimAl, RAxML
+For example, https://anaconda.org/bioconda/dendropy
+conda install -c bioconda dendropy
+. However, for P4 and USEARCH which is not easy to set up.
+<code>
+# USEARCH
+https://www.drive5.com/usearch/download.html
+chmod +x /usr/bin/usearch6.0.98_i86linux32
+export PATH=/misc/scratch2/xizhang/PhyloTol/Conda:$PATH
+</code>
+<code>
+# P4
+https://p4.nhm.ac.uk/installation.html
+conda install scipy gsl nlopt bitarray
+https://github.com/pgfoster/p4-phylogenetics
+export PYTHONPATH=$PYTHONPATH:/misc/scratch2/xizhang/PhyloTol/Conda/p4-phylogenetics-master
+export PATH=$PATH:/misc/scratch2/xizhang/PhyloTol/Conda/p4-phylogenetics-master/bin
+must change the hardcoded path in setup.py
+my_include_dirs = ["/home/xizhang/.conda/envs/PhyloToL/include"]
+my_lib_dirs = ["/home/xizhang/.conda/envs/PhyloToL/lib"]
+conda install -c conda-forge nlopt
+conda install -c anaconda bitarray
+python3 setup.py build_ext -i
+p4 -help
+</code>
+. With all these done, user can yield an yaml file.
+conda env export > PhyloToL.yml
+<code>
+name: PhyloToL
+channels:
+  - bioconda
+  - anaconda
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=main
+  - _openmp_mutex=4.5=1_gnu
+  - asttokens=2.0.5=pyhd8ed1ab_0
+  - biopython=1.79=py36h8f6f2f9_0
+  - bitarray=1.6.0=py36h7b6447c_0
+  - ca-certificates=2020.10.14=0
+  - certifi=2020.6.20=py36_0
+  - dendropy=4.5.2=pyh3252c3a_0
+  - executing=0.8.2=pyhd8ed1ab_0
+  - ld_impl_linux-64=2.35.1=h7274673_9
+  - libblas=3.9.0=11_linux64_openblas
+  - libcblas=3.9.0=11_linux64_openblas
+  - libffi=3.3=he6710b0_2
+  - libgcc=7.2.0=h69d50b8_2
+  - libgcc-ng=9.3.0=h5101ec6_17
+  - libgfortran-ng=11.2.0=h69a702a_12
+  - libgfortran5=11.2.0=h5c6108e_12
+  - libgomp=9.3.0=h5101ec6_17
+  - liblapack=3.9.0=11_linux64_openblas
+  - libopenblas=0.3.17=pthreads_h8fe5266_1
+  - libstdcxx-ng=9.3.0=hd4cf53a_17
+  - mafft=7.310=h1b792b2_4
+  - ncurses=6.3=h7f8727e_2
+  - nlopt=2.7.0=py36he9b8a8a_1
+  - numpy=1.19.5=py36hfc0c790_2
+  - openssl=1.1.1m=h7f8727e_0
+  - perl=5.26.2=h14c3975_0
+  - perl-bioperl=1.6.924=4
+  - perl-threaded=5.32.1=hdfd78af_1
+  - perl-yaml=1.29=pl526_0
+  - pip=21.2.2=py36h06a4308_0
+  - python=3.6.13=h12debd9_1
+  - python-devtools=0.8.0=pyhd8ed1ab_0
+  - python_abi=3.6=2_cp36m
+  - raxml=8.2.12=h779adbc_3
+  - readline=8.1.2=h7f8727e_1
+  - setuptools=58.0.4=py36h06a4308_0
+  - six=1.16.0=pyh6c4a22f_0
+  - sqlite=3.37.0=hc218d9a_0
+  - tk=8.6.11=h1ccaba5_0
+  - trimal=1.4.1=h7d875b9_5
+  - wheel=0.37.1=pyhd3eb1b0_0
+  - xz=5.2.5=h7b6447c_0
+  - zlib=1.2.11=h7f8727e_4
+prefix: /home/xizhang/.conda/envs/PhyloToL
+</code>
+**Execute Yaml file**
+ With this yaml file on hand, the new user can easily install PhyloToL software dependencies(except P4 and USEARCH) via below.
+<code>
+source ~/.bashrc
+#
+# To activate this environment, use
+#
+# $ conda activate PhyloToL
+#
+# To deactivate an active environment, use
+#
+# $ conda deactivate
+</code>
+<Last updated by Xi Zhang on Feb 8th,2022>