From 4f14d592277d4bd3af98f2299e5e2e1d48a32016 Mon Sep 17 00:00:00 2001
From: nikos <n.pappas@uu.nl>
Date: Thu, 7 Jan 2021 16:04:31 +0100
Subject: [PATCH] added procedures for building containers
---
resources/singularity/rafah/README.md | 57 ++
resources/singularity/rafah/rafah.def | 58 ++
resources/singularity/vhmnet/README.md | 53 ++
resources/singularity/vhmnet/environment.txt | 112 ++++
resources/singularity/vhulk/README.md | 73 +++
resources/singularity/vhulk/vHULK-v0.1.py | 516 ++++++++++++++++++
resources/singularity/vhulk/vhulk.def | 56 ++
.../singularity/vhulk/vhulk_explicit.txt | 375 +++++++++++++
resources/singularity/wish/README.md | 32 ++
resources/singularity/wish/wish.def | 45 ++
10 files changed, 1377 insertions(+)
create mode 100644 resources/singularity/rafah/README.md
create mode 100644 resources/singularity/rafah/rafah.def
create mode 100644 resources/singularity/vhmnet/README.md
create mode 100644 resources/singularity/vhmnet/environment.txt
create mode 100644 resources/singularity/vhulk/README.md
create mode 100755 resources/singularity/vhulk/vHULK-v0.1.py
create mode 100644 resources/singularity/vhulk/vhulk.def
create mode 100644 resources/singularity/vhulk/vhulk_explicit.txt
create mode 100644 resources/singularity/wish/README.md
create mode 100644 resources/singularity/wish/wish.def
diff --git a/resources/singularity/rafah/README.md b/resources/singularity/rafah/README.md
new file mode 100644
index 0000000..93a7e19
--- /dev/null
+++ b/resources/singularity/rafah/README.md
@@ -0,0 +1,57 @@
+# RaFaH
+
+Available from `library://papanikos_182/default/rafah:0.1`
+
+## Procedure
+
+0. Create a new dir for build context and get in there
+
+1. Grab necessary dependencies from the
+[RaFaH repo](https://sourceforge.net/projects/rafah/files/RaFAH_v0.1_Files/)
+
+```
+$ wget https://sourceforge.net/projects/rafah/files/RaFAH_v0.1_Files
+$ tar -xzvf whatever_is_downloaded
+```
+
+> wgetting is slow, I used another copy, locally available
+
+2. Edit RaFaH script to point to appropriate locations in the container
+ - Replace shebang (line 1) with `#!/usr/bin/env perl`
+ - Change line 37 to `my $valid_domains_file = "/opt/resources/HP_Ranger_Model_3_Valid_Cols.txt";`
+ - Change line 38 to `my $hmm_models_prefix = "/opt/resources/HP_Ranger_Model_3_Filtered_0.9_Valids.hmm";`
+ - Change line 39 to `my $r_script_file_name = "/src/Predict_Host_RF.R";`
+ - Change line 40 to `my $r_model_file_name = "/opt/resources/MMSeqs_Clusters_Ranger_Model_1+2+3_Clean.RData";`
+
+3. Make RaFah_v0.1.pl executable
+```
+$ chmod +x RaFaH_v0.1.pl
+```
+
+4. Bundle tables and models in a tar archive (not the perl and R script) and
+not the `HP_Ranger_Model_3_Valid_Cols.txt`
+```
+$ tar -czvf rafah_resources.tar.gz ./*hmm* MMSeqs_Clusters_Ranger_Model_1+2+3_Clean.RData
+```
+
+5. Build the image with the definition file
+```
+$ sudo singularity build rafah.sif rafah.def
+```
+
+6. [Optional] Sign the image
+```
+$ singularity sign rafah.sif
+```
+
+7. Push it on the cloud
+```
+$ singulairty push rafah.sif library://papanikos_182/default/rafah:0.1
+```
+
+## Usage
+
+```
+$ singularity run library://papanikos_182/default/rafah:0.1 RaFaH_v0.1.pl -h
+```
+
diff --git a/resources/singularity/rafah/rafah.def b/resources/singularity/rafah/rafah.def
new file mode 100644
index 0000000..66007c2
--- /dev/null
+++ b/resources/singularity/rafah/rafah.def
@@ -0,0 +1,58 @@
+Bootstrap: docker
+From: continuumio/miniconda3
+
+%labels
+ Author "Felipe Coutinho"
+ Maintainer papanikos_182
+ Version 0.1
+ Source https://sourceforge.net/projects/rafah/
+ Preprint https://www.biorxiv.org/content/10.1101/2020.09.25.313155v1
+
+%files
+ RaFAH_v0.1.pl /opt/conda/bin/
+ Predict_Host_RF.R /src/
+ HP_Ranger_Model_3_Valid_Cols.txt /opt/HP_Ranger_Model_3_Valid_Cols.txt
+ rafah_resources.tar.gz /opt/rafah_resources.tar.gz
+
+%environment
+ export PATH=/src:$PATH
+
+%post
+ # Update OS
+ apt update && apt upgrade -y
+
+ # Set up resources dirs for running RaFAH
+ mkdir -p /opt/resources
+ mv /opt/HP_Ranger_Model_3_Valid_Cols.txt /opt/resources
+ tar -xzvf /opt/rafah_resources.tar.gz -C /opt/resources && rm /opt/rafah_resources.tar.gz
+
+ # Install dependencies
+ conda config --add channels conda-forge
+ conda config --add channels default
+ conda config --add channels bioconda
+ conda config --add channels r
+ conda update -y conda
+ conda install -y mamba
+ mamba install -y r=3.6 r-ranger perl-bioperl hmmer=3.1b2 prodigal=2.6
+ conda clean --all -y
+
+
+%help
+ A container for RaFAH v0.1 [https://sourceforge.net/projects/rafah].
+ Main perl script is in /src .
+ Helper R script for models is in /src .
+ Required data dependencies are stored in /opt/resources.
+
+ To run the help menu from RaFAH from this container execute
+
+ $ singularity exec shub://papanikos_182/rafah:0.1 perl RaFAH_v0.1.pl --help
+
+ To run an anlysis for all genomes stored in the /path/to/genomes/ (last slash is required),
+ with all files ending with .fasta and store the results in
+ /path/to/outdir/prefix (several files will be written in the /path/to/outdir and prefixed with prefix_ ).
+
+ $ singularity exec shub://papanikos_182/rafah:0.1 \
+ perl RaFAH_v0.1.pl \
+ --genomes_dir /path/to/genomes/ \
+ --extension fasta \
+ --file_prefix /path/to/outdir/prefix
diff --git a/resources/singularity/vhmnet/README.md b/resources/singularity/vhmnet/README.md
new file mode 100644
index 0000000..7e97509
--- /dev/null
+++ b/resources/singularity/vhmnet/README.md
@@ -0,0 +1,53 @@
+# VirHostMatcher-Net
+
+Available from `library://papanikos_182/default/vhmnet:0.1`
+
+* Note that data dependencies are not included in the container.
+You need to get them with
+```
+wget -c http://www-rcf.usc.edu/~weiliw/VirHostMatcher-Net/data_VirHostMatcher-Net_both_modes.tar.gz
+tar xf data_VirHostMatcher-Net_both_modes.tar.gz
+```
+The models and genomes unpacked are 125G.
+
+* [My fork](https://github.com/papanikos/VirHostMatcher-Net)
+is used for grabbing source. It mainly allows to define a directory
+where the data are located
+
+## Procedure
+
+0. Create a new dir for build context and get in there
+
+1. Create a conda env with its requirements, verify it is working and export
+it explicitly
+
+```
+$ conda env create -n vhmnet numpy pandas biopython blast
+...
+...Test it runs...
+...
+$ conda list -n vhmnet --explicit > environment.txt
+```
+
+2. Build the image with the definition file
+```
+$ sudo singularity build vhmnet.sif vhmnet.def
+```
+
+3. [Optional] Sign the image
+```
+$ singularity sign vhmnet.sif
+```
+
+4. Push it on the cloud
+```
+$ singulairty push vhmnet.sif library://papanikos_182/default/vhmnet:0.1
+```
+
+## Usage
+
+```
+$ singularity run library://papanikos_182/default/vhmnet:0.1 \
+ VirHostMatcher.py -h
+```
+
diff --git a/resources/singularity/vhmnet/environment.txt b/resources/singularity/vhmnet/environment.txt
new file mode 100644
index 0000000..fc21c7b
--- /dev/null
+++ b/resources/singularity/vhmnet/environment.txt
@@ -0,0 +1,112 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
+https://repo.anaconda.com/pkgs/main/linux-64/ca-certificates-2020.12.8-h06a4308_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.35.1-hed1e6ac_1.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran4-7.5.0-hae1eefd_17.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-ng-9.3.0-h2ae2ef3_17.tar.bz2
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2020f-he74cb21_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/libgfortran-ng-7.5.0-hae1eefd_17.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-9.3.0-h5dbcf3e_17.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-1_gnu.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-9.3.0-h5dbcf3e_17.tar.bz2
+https://repo.anaconda.com/pkgs/main/linux-64/bzip2-1.0.8-h7b6447c_0.conda
+https://repo.anaconda.com/pkgs/main/linux-64/expat-2.2.10-he6710b0_2.conda
+https://repo.anaconda.com/pkgs/main/linux-64/libffi-3.3-he6710b0_2.conda
+https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.12-pthreads_hb3c22a3_1.tar.bz2
+https://repo.anaconda.com/pkgs/main/linux-64/ncurses-6.2-he6710b0_1.conda
+https://repo.anaconda.com/pkgs/main/linux-64/openssl-1.1.1i-h27cfd23_0.conda
+https://repo.anaconda.com/pkgs/main/linux-64/pcre-8.44-he6710b0_0.conda
+https://repo.anaconda.com/pkgs/main/linux-64/perl-5.26.2-h14c3975_0.conda
+https://repo.anaconda.com/pkgs/main/linux-64/xz-5.2.5-h7b6447c_0.conda
+https://repo.anaconda.com/pkgs/main/linux-64/zlib-1.2.11-h7b6447c_3.conda
+https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-6_openblas.tar.bz2
+https://repo.anaconda.com/pkgs/main/linux-64/libedit-3.1.20191231-h14c3975_1.conda
+https://repo.anaconda.com/pkgs/main/linux-64/libssh2-1.9.0-h1ba5d50_1.conda
+https://conda.anaconda.org/bioconda/linux-64/perl-app-cpanminus-1.7044-pl526_1.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-base-2.23-pl526_1.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-common-sense-3.74-pl526_2.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-compress-raw-bzip2-2.087-pl526he1b5a44_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-compress-raw-zlib-2.087-pl526hc9558a2_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-constant-1.33-pl526_1.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-data-dumper-2.173-pl526_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-digest-hmac-1.03-pl526_3.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-digest-md5-2.55-pl526_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-exporter-5.72-pl526_1.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-exporter-tiny-1.002001-pl526_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-extutils-makemaker-7.36-pl526_1.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-html-tagset-3.20-pl526_3.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-io-html-1.001-pl526_2.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-io-zlib-1.10-pl526_2.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-mozilla-ca-20180117-pl526_1.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-parent-0.236-pl526_1.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-scalar-list-utils-1.52-pl526h516909a_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-socket-2.027-pl526_1.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-try-tiny-0.30-pl526_1.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/perl-xml-parser-2.44_01-pl526ha1d75be_1002.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-xml-sax-base-1.09-pl526_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-xsloader-0.24-pl526_0.tar.bz2
+https://repo.anaconda.com/pkgs/main/linux-64/readline-8.0-h7b6447c_0.conda
+https://repo.anaconda.com/pkgs/main/linux-64/tk-8.6.10-hbc83047_0.conda
+https://repo.anaconda.com/pkgs/main/linux-64/krb5-1.18.2-h173b8e3_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-6_openblas.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/liblapack-3.9.0-6_openblas.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-carp-1.38-pl526_3.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-encode-2.88-pl526_1.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-file-path-2.16-pl526_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-html-parser-3.72-pl526h6bb024c_5.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-io-compress-2.087-pl526he1b5a44_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-list-moreutils-xs-0.428-pl526_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-mime-base64-3.15-pl526_1.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-ntlm-1.09-pl526_4.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-storable-3.15-pl526h14c3975_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-test-requiresinternet-0.05-pl526_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-types-serialiser-1.0-pl526_2.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-xml-namespacesupport-1.12-pl526_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/sqlite-3.34.0-h74cdb3f_0.tar.bz2
+https://repo.anaconda.com/pkgs/main/linux-64/libcurl-7.71.1-h20c2e04_1.conda
+https://conda.anaconda.org/bioconda/linux-64/perl-business-isbn-data-20140910.003-pl526_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-encode-locale-1.05-pl526_6.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-file-temp-0.2304-pl526_2.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-html-tree-5.07-pl526_1.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-json-xs-2.34-pl526h6bb024c_3.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-list-moreutils-0.428-pl526_1.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-lwp-mediatypes-6.04-pl526_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-net-ssleay-1.88-pl526h90d6eec_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-pathtools-3.75-pl526h14c3975_1.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-time-local-1.28-pl526_1.tar.bz2
+https://repo.anaconda.com/pkgs/main/linux-64/python-3.9.1-hdb3f193_2.conda
+https://repo.anaconda.com/pkgs/main/linux-64/certifi-2020.12.5-py39h06a4308_0.conda
+https://repo.anaconda.com/pkgs/main/linux-64/curl-7.71.1-hbc83047_1.conda
+https://conda.anaconda.org/bioconda/linux-64/perl-archive-tar-2.32-pl526_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-business-isbn-3.004-pl526_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-http-date-6.02-pl526_3.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-io-socket-ssl-2.066-pl526_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-json-4.02-pl526_0.tar.bz2
+https://conda.anaconda.org/bioconda/noarch/perl-xml-sax-1.02-pl526_0.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/python_abi-3.9-1_cp39.tar.bz2
+https://repo.anaconda.com/pkgs/main/noarch/pytz-2020.5-pyhd3eb1b0_0.conda
+https://repo.anaconda.com/pkgs/main/linux-64/six-1.15.0-py39h06a4308_0.conda
+https://repo.anaconda.com/pkgs/main/noarch/wheel-0.36.2-pyhd3eb1b0_0.conda
+https://conda.anaconda.org/conda-forge/linux-64/numpy-1.19.4-py39hdbf815f_2.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-file-listing-6.04-pl526_1.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-uri-1.76-pl526_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-xml-sax-expat-0.51-pl526_3.tar.bz2
+https://repo.anaconda.com/pkgs/main/noarch/python-dateutil-2.8.1-py_0.conda
+https://repo.anaconda.com/pkgs/main/linux-64/setuptools-51.0.0-py39h06a4308_2.conda
+https://conda.anaconda.org/conda-forge/linux-64/biopython-1.78-py39hbd71b63_1.tar.bz2
+https://conda.anaconda.org/conda-forge/linux-64/pandas-1.2.0-py39hde0f152_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-http-message-6.18-pl526_0.tar.bz2
+https://conda.anaconda.org/bioconda/noarch/perl-net-http-6.19-pl526_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-www-robotrules-6.02-pl526_3.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-xml-simple-2.25-pl526_1.tar.bz2
+https://repo.anaconda.com/pkgs/main/linux-64/pip-20.3.3-py39h06a4308_0.conda
+https://conda.anaconda.org/bioconda/linux-64/perl-http-cookies-6.04-pl526_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-http-daemon-6.01-pl526_1.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-http-negotiate-6.01-pl526_3.tar.bz2
+https://conda.anaconda.org/bioconda/noarch/perl-libwww-perl-6.39-pl526_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/perl-lwp-protocol-https-6.07-pl526_4.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/entrez-direct-13.9-pl526h375a9b1_0.tar.bz2
+https://conda.anaconda.org/bioconda/linux-64/blast-2.10.1-pl526he19e7b1_3.tar.bz2
diff --git a/resources/singularity/vhulk/README.md b/resources/singularity/vhulk/README.md
new file mode 100644
index 0000000..500802a
--- /dev/null
+++ b/resources/singularity/vhulk/README.md
@@ -0,0 +1,73 @@
+# RaFaH
+
+Available from `library://papanikos_182/default/vhulk:0.1`
+
+## Procedure
+
+0. Create a new dir for build context and get in there
+
+1. Grab source from the
+[vHULK repo](https://github.com/LaboratorioBioinformatica/vHULK)
+
+
+```
+$ git clone https://github.com/LaboratorioBioinformatica/vHULK.git
+```
+
+2. Create a conda env as per
+[their suggestions](https://github.com/LaboratorioBioinformatica/vHULK#dependencies)
+and export it explicitly with
+```
+$ conda list -n vhulk --explicit > vhulk_explicit.txt
+```
+This can be used for running stuff
+
+3. Grab its data dependencies with the auxiliary script they provide
+```
+$ conda activate vhulk
+(vhulk) $ python ./download_and_set_models.py
+```
+
+4. Extract (for testing) and rebundle under `vhulk_resources.tar.gz`. This
+archive contains
+```
+$ tar -tvf vhulk_resources.tar.gz
+
+drwxr-xr-x nikos/binf 0 2020-12-15 12:21 models/
+-rw-r----- nikos/binf 70143964 2020-09-15 00:52 models/model_species_total_fixed_relu_08mar_2020.h5
+-rw-r----- nikos/binf 70165848 2020-09-15 00:52 models/model_genus_total_fixed_relu_08mar_2020.h5
+-rw-r--r-- nikos/binf 175382277 2020-12-15 12:19 models/all_vogs_hmm_profiles_feb2018.hmm.h3f
+-rw-r----- nikos/binf 70165848 2020-09-15 00:52 models/model_genus_total_fixed_softmax_01mar_2020.h5
+-rw-r----- nikos/binf 70143964 2020-09-15 00:52 models/model_species_total_fixed_softmax_01mar_2020.h5
+-rw-r--r-- nikos/binf 333265 2020-12-15 12:19 models/all_vogs_hmm_profiles_feb2018.hmm.h3i
+-rw-r--r-- nikos/binf 374382899 2020-12-15 12:19 models/all_vogs_hmm_profiles_feb2018.hmm.h3p
+-rw-r--r-- nikos/binf 767855419 2020-12-15 12:19 models/all_vogs_hmm_profiles_feb2018.hmm
+-rw-r--r-- nikos/binf 317721714 2020-12-15 12:19 models/all_vogs_hmm_profiles_feb2018.hmm.h3m
+```
+
+5. Modify the `vHULK-v0.1.py` to mainly point to the appropriate locations
+in the container. The rest is aesthetics done with
+[black](https://github.com/psf/black). Also make it executable.
+The copy in here is the one used in the container.
+
+6. Build the image with the definition file
+```
+$ sudo singularity build vhulk.sif vhulk.def
+```
+
+7. [Optional] Sign the image
+```
+$ singularity sign vhulk.sif
+```
+
+8. Push it on the cloud
+```
+$ singulairty push vhulk.sif library://papanikos_182/default/vhulk:0.1
+```
+
+## Usage
+
+```
+$ singularity run library://papanikos_182/default/vhulk:0.1 vHULK_v0.1.py -h
+```
+
diff --git a/resources/singularity/vhulk/vHULK-v0.1.py b/resources/singularity/vhulk/vHULK-v0.1.py
new file mode 100755
index 0000000..b509fbf
--- /dev/null
+++ b/resources/singularity/vhulk/vHULK-v0.1.py
@@ -0,0 +1,516 @@
+#!/usr/bin/env python
+# coding: utf-8
+# Edited May, 27th 2020
+## This is vHULK: viral Host Unveiling Kit
+# Developed by Deyvid Amgarten and Bruno Iha
+# Creative commons
+
+# Import required Python modules
+import numpy as np
+import pandas as pd
+from Bio import SeqIO
+import re
+import sys
+import os
+
+os.environ["TF_CPP_MIN_LOG_LEVEL"] = "3"
+import subprocess
+import datetime
+import argparse
+import warnings
+import csv
+
+warnings.filterwarnings("ignore", category=DeprecationWarning)
+warnings.simplefilter(action="ignore", category=FutureWarning)
+
+from time import gmtime, strftime
+from tensorflow.keras.layers import Dense, Activation, LeakyReLU, ReLU
+from tensorflow.keras.models import load_model
+from scipy.special import entr
+
+
+# Function declarations
+# Run prokka
+def run_prokka(binn, input_folder, threads):
+ # Check the fasta format
+ prefix = get_prefix(binn)
+ # Filehandle where the output of prokka will be saved
+ # output_prokka = open(str(prefix)+'prokka.output', mode='w')
+ # Full command line for prokka
+ command_line = (
+ "prokka --kingdom Viruses --centre X --compliant --gcode 11 --cpus "
+ + threads
+ + " --force --quiet --prefix prokka_results_"
+ + str(prefix)
+ + " --fast --norrna --notrna --outdir "
+ + input_folder
+ + "results/prokka/"
+ + str(prefix)
+ + " --cdsrnaolap --noanno "
+ + input_folder
+ + str(binn)
+ ).split()
+ return_code = subprocess.call(command_line, stderr=subprocess.PIPE)
+ # Check with prokka run smothly
+ if return_code == 1:
+ print("Prokka may not be correctly installed. Please check that.")
+ sys.exit(1)
+
+
+# Get prefix from bins
+def get_prefix(binn):
+ if re.search(".fasta", binn):
+ prefix = re.sub(".fasta", "", binn)
+ else:
+ prefix = re.sub(".fa", "", binn)
+ return prefix
+
+
+# Extract Matrix
+
+
+###
+### Main code
+###
+
+# Set arguments
+# Modification to use argparse
+parser = argparse.ArgumentParser(
+ description="Predict phage draft genomes in metagenomic bins."
+)
+parser.add_argument(
+ "-i",
+ action="store",
+ required=True,
+ dest="input_folder",
+ help="Path to a folder containing metagenomic bins in .fa or .fasta format (required!)",
+)
+parser.add_argument(
+ "-t",
+ action="store",
+ dest="threads",
+ default="1",
+ help="Number of CPU threads to be used by Prokka and hmmscan (default=1)",
+)
+args = parser.parse_args()
+
+
+# Greeting message
+print("\n**Welcome v.HULK, a toolkit for phage host prediction!\n")
+
+
+# Verify databases
+if not os.path.isfile("/opt/vHULK/models/all_vogs_hmm_profiles_feb2018.hmm"):
+ print(
+ "**Your database and models are not set. Please, run: python download_and_set_models.py \n"
+ )
+ sys.exit(1)
+
+
+# Create Filehandle for warnings
+# warnings_handle = open('marvel-warnings.txt', 'w')
+
+# Important variables
+input_folder = args.input_folder
+threads = args.threads
+
+# Fix input folder path if missing '/'
+if not re.search("/$", input_folder):
+ input_folder = input_folder + "/"
+
+
+# Take the input folder and list all multifasta (bins) contained inside it
+# print(input_folder)
+list_bins_temp = os.listdir(input_folder)
+list_bins = []
+count_bins = 0
+# Empty folder
+if list_bins_temp == []:
+ print("**Input folder is empty. Exiting...\n")
+ sys.exit(1)
+else:
+ for each_bin in list_bins_temp:
+ if re.search(".fasta$", each_bin, re.IGNORECASE):
+ list_bins.append(each_bin)
+ count_bins += 1
+ elif re.search(".fa$", each_bin, re.IGNORECASE):
+ list_bins.append(each_bin)
+ count_bins += 1
+
+if count_bins == 0:
+ print(
+ "**There is no valid genome inside the input folder (%s).\n\
+ Genome or bins should be in '.fasta' or '.fa' format.\nExiting..."
+ % input_folder
+ )
+ sys.exit(1)
+
+print(
+ "**Arguments are OK. Checked the input folder and found %d genomes.\n"
+ % count_bins
+)
+print("**" + str(datetime.datetime.now()))
+
+# Create results folder
+try:
+ os.stat(input_folder + "results/")
+except:
+ os.mkdir(input_folder + "results/")
+
+
+#####
+# PROKKA
+#####
+# Running prokka for all the bins multfasta files in input folder
+# Perform a check in each bin, then call the execute_prokka function individually
+# It may take awhile
+count_prokka = 0
+print("**Prokka has started, this may take awhile. Be patient.\n")
+for binn in list_bins:
+ # Verify bin/Genome size
+ len_bin = 0
+ for record in SeqIO.parse(input_folder + binn, "fasta"):
+ len_bin += len(record.seq)
+ # If a bin/genome is too short, skip it
+ if len_bin < 5000:
+ print(
+ "**v.HULK has found a genome or bin, which is too short to code \
+ proteins (<5000pb). As CDSs are an important feature for v.HULK, \
+ we will be skipping this: "
+ + binn
+ )
+ continue
+ run_prokka(binn, input_folder, threads)
+ count_prokka += 1
+ if count_prokka % 10 == 0:
+ print("**Done with %d genomes..." % count_prokka)
+print("**Prokka tasks have finished!\n")
+
+
+####
+# HMM SEARCHES
+####
+print("**" + str(datetime.datetime.now()))
+print("**Starting HMM scan, this may take awhile. Be patient.\n")
+# print(str(datetime.datetime.now()))
+# Create a new results folder for hmmscan output
+try:
+ os.stat(input_folder + "results/hmmscan/")
+except:
+ os.mkdir(input_folder + "results/hmmscan/")
+
+# Call HMMscan to all genomes
+dic_matrices_by_genome = {}
+prop_hmms_hits = {}
+count_hmm = 0
+for binn in list_bins:
+ # Prefix for naming results
+ prefix = get_prefix(binn)
+ command_line_hmmscan = (
+ "hmmscan -o "
+ + input_folder
+ + "results/hmmscan/"
+ + prefix
+ + "_hmmscan.out --cpu "
+ + threads
+ + " --tblout "
+ + input_folder
+ + "results/hmmscan/"
+ + prefix
+ + "_hmmscan.tbl --noali /opt/vHULK/models/all_vogs_hmm_profiles_feb2018.hmm "
+ + input_folder
+ + "results/prokka/"
+ + prefix
+ + "/prokka_results_"
+ + prefix
+ + ".faa"
+ )
+ # print(command_line_hmmscan)
+ # Use -E 1 for next time running HMMscan or leave the fix down there
+ # In case hmmscan returns an error - Added only because it stopped in half
+ # if os.path.exists(input_folder + 'results/hmmscan/' + prefix + '_hmmscan.tbl'):
+ # continue
+ try:
+ subprocess.call(command_line_hmmscan, shell=True)
+ # Comment line above and uncomment line below in case you want to run v.HULK without running hmmscan all over again
+ # True
+ except:
+ print("**Error calling HMMscan:", command_line_hmmscan)
+ sys.exit(1)
+ count_hmm += 1
+ # Iteration control
+ print("**Done with %d bins HMM searches..." % count_hmm)
+ ## Create dictionary as ref of collumns - pVOGs
+ dic_vogs_headers = {}
+ with open("/opt/vHULK/files/VOGs_header.txt", "r") as file2:
+ for line2 in file2:
+ key = re.match("(.+)\n", line2).group(1)
+ dic_vogs_headers[key] = np.float32(0.0)
+ #
+ # Parse hmmscan results by gene
+ num_proteins_bin = 0
+ with open(
+ input_folder
+ + "results/prokka/"
+ + prefix
+ + "/prokka_results_"
+ + prefix
+ + ".faa",
+ "r",
+ ) as faa:
+ for line in faa:
+ if re.search("^>", line):
+ num_proteins_bin += 1
+ # Get gene name here
+ gene_name = re.search("^>(.*)", line).group(1)
+ dic_matches = {}
+
+ # Parse hmmout
+ with open(
+ input_folder + "results/hmmscan/" + prefix + "_hmmscan.tbl", "r"
+ ) as hmmscan_out:
+ dic_genes_scores = {}
+ for line in hmmscan_out:
+ vog = ""
+ gene = ""
+ evalue = np.float32(0.0)
+ score = np.float32(0.0)
+ bias = np.float32(0.0)
+ if re.match("^VOG", line):
+ matches = re.match(
+ "^(VOG[\d\w]+)\s+-\s+([^\s]+)[^\d]+([^\s]+)\s+([^\s]+)\s+([^\s]+)",
+ line,
+ )
+ vog = matches[1]
+ gene = matches[2]
+ evalue = float(matches[3])
+ score = float(matches[4])
+ bias = float(matches[5])
+ if gene in dic_genes_scores:
+ dic_genes_scores[gene].append([vog, evalue, score, bias])
+ else:
+ dic_genes_scores[gene] = [[vog, evalue, score, bias]]
+ # Here goes the continuation
+ # Create a matrix by accession
+ dic_matrices_by_genome[prefix] = pd.DataFrame(
+ index=dic_genes_scores.keys(),
+ columns=dic_vogs_headers.keys(),
+ dtype=float,
+ )
+ dic_matrices_by_genome[prefix].fillna(value=np.float32(0.0), inplace=True)
+ # Fill in evalue values
+ for gene in dic_genes_scores:
+ for each_match in dic_genes_scores[gene]:
+ # print(each_match[1], gene)
+ # Fix for evalue values greater than 1
+ if each_match[1] > 1:
+ # print(each_match[1])
+ each_match[1] = 1
+ # print(each_match[1])
+ dic_matrices_by_genome[prefix][each_match[0]][gene] = np.float32(
+ 1.0
+ ) - np.float32(each_match[1])
+print("\n**HMMscan has finished.")
+
+# Condense matrices to array by suming up columns
+list_condensed_matrices = []
+list_file_names = []
+for matrix in dic_matrices_by_genome:
+ temp = list(dic_matrices_by_genome[matrix].sum(axis=0, skipna=True))
+ list_file_names.append(matrix)
+ # Parse tag
+ # if re.search('^NC_.*', matrix):
+ # matrix = matrix.replace("NC_", "NC")
+ # [0]accession [1]genus [2]species
+ # tags = matrix.split("_")
+ # For Genus
+ # temp.append(tags[1])
+ # temp.append(tags[0])
+ # For Species
+ # temp.append(tag[1]+"_"+tag[2])
+ # temp.append(tag[0])
+ list_condensed_matrices.append(temp)
+
+# Convert to array
+# import numpy as np
+array = np.array(list_condensed_matrices)
+# print("ARRAY-SHAPE: ", len(array))
+
+###
+# Predictions
+###
+
+print("\n**Starting deeplearning predictions...")
+# load models
+model_genus_relu = load_model(
+ "/opt/vHULK/models/model_genus_total_fixed_relu_08mar_2020.h5",
+ custom_objects={"LeakyReLU": LeakyReLU, "ReLU": ReLU},
+)
+model_genus_sm = load_model(
+ "/opt/vHULK/models/model_genus_total_fixed_softmax_01mar_2020.h5",
+ custom_objects={"LeakyReLU": LeakyReLU, "ReLU": ReLU},
+)
+model_species_relu = load_model(
+ "/opt/vHULK/models/model_species_total_fixed_relu_08mar_2020.h5",
+ custom_objects={"LeakyReLU": LeakyReLU, "ReLU": ReLU},
+)
+model_species_sm = load_model(
+ "/opt/vHULK/models/model_species_total_fixed_softmax_01mar_2020.h5",
+ custom_objects={"LeakyReLU": LeakyReLU, "ReLU": ReLU},
+)
+
+with open(input_folder + "results/results.csv", "w") as file:
+ file.write(
+ "BIN/genome,pred_genus_relu,score_genus_relu,Pred_genus_softmax,score_genus_softmax,pred_species_relu,score_species_relu,pred_species_softmax,score_species_softmax,final_prediction,entropy\n"
+ )
+
+for i in range(0, len(array)):
+ # Genus ReLu
+ # print(list_file_names[i])
+ pred_gen_relu = model_genus_relu.predict(np.array([array[i]]))
+ # print("Genus:ReLu")
+ # print(pred_gen_relu)
+ position_pred_gen_relu = np.argmax(pred_gen_relu)
+ if not pred_gen_relu.any():
+ name_pred_gen_relu = "None"
+ score_pred_gen_relu = "0"
+ else:
+ list_hosts_genus = [
+ line.rstrip("\n") for line in open("/opt/vHULK/files/list_hosts_genus.txt")
+ ]
+ name_pred_gen_relu = list_hosts_genus[position_pred_gen_relu]
+ score_pred_gen_relu = str(pred_gen_relu[0][position_pred_gen_relu])
+ # print(list_hosts_genus[position_pred_gen_relu])
+ # print(position_pred_gen_relu, pred_gen_relu[0][position_pred_gen_relu])
+
+ # Genus softmax
+ pred_gen_sm = model_genus_sm.predict(np.array([array[i]]))
+ # print("Genus:Softmax")
+ # print(pred_gen_sm)
+ position_pred_gen_sm = np.argmax(pred_gen_sm)
+ list_hosts_genus = [
+ line.rstrip("\n") for line in open("/opt/vHULK/files/list_hosts_genus.txt")
+ ]
+ name_pred_gen_sm = list_hosts_genus[position_pred_gen_sm]
+ score_pred_gen_sm = str(pred_gen_sm[0][position_pred_gen_sm])
+ # print(list_hosts_genus[position_pred_gen_sm])
+ # print(position_pred_gen_sm, pred_gen_sm[0][position_pred_gen_sm])
+
+ # Species Relu
+ pred_sp_relu = model_species_relu.predict(np.array([array[i]]))
+ # print("Species:ReLu")
+ # print(pred_sp_relu)
+ position_pred_sp_relu = np.argmax(pred_sp_relu)
+ if not pred_sp_relu.any():
+ name_pred_sp_relu = "None"
+ score_pred_sp_relu = "0"
+ else:
+ list_hosts_sp = [
+ line.rstrip("\n") for line in open("/opt/vHULK/files/list_hosts_species.txt")
+ ]
+ # print(list_hosts_sp)
+ name_pred_sp_relu = list_hosts_sp[position_pred_sp_relu]
+ score_pred_sp_relu = str(pred_sp_relu[0][position_pred_sp_relu])
+ # print(list_hosts_sp[position_pred_sp_relu])
+ # print(position_pred_sp_relu, pred_sp_relu[0][position_pred_sp_relu])
+
+ # Species softmax
+ pred_sp_sm = model_species_sm.predict(np.array([array[i]]))
+ # print("Species:Softmax")
+ # print(pred_sp_sm)
+ position_pred_sp_sm = np.argmax(pred_sp_sm)
+ list_hosts_sp = [
+ line.rstrip("\n") for line in open("/opt/vHULK/files/list_hosts_species.txt")
+ ]
+ # print(list_hosts_sp)
+ name_pred_sp_sm = list_hosts_sp[position_pred_sp_sm]
+ score_pred_sp_sm = str(pred_sp_sm[0][position_pred_sp_sm])
+ # print(list_hosts_sp[position_pred_sp_sm])
+ # print(position_pred_sp_sm, pred_sp_sm[0][position_pred_sp_sm])
+ ##
+ # Calculate entropy
+ entropy_genus_sm = entr(pred_gen_sm).sum(axis=1)
+ # entropy_genus_sm = "{:.7f}".format(entr(pred_gen_sm).sum(axis=1))
+ #
+ # Apply decision tree
+ #
+ final_decision = "None"
+ # Relu sp
+ if float(score_pred_sp_relu) > 0.9:
+ final_decision = name_pred_sp_relu
+ # SM sp
+ if float(score_pred_sp_sm) > 0.6 and name_pred_sp_sm != final_decision:
+ final_decision = name_pred_sp_sm
+ # Coudn't predict species
+ if final_decision == "None":
+ # Put here sm sp
+ if float(score_pred_sp_sm) > 0.6:
+ final_decision = name_pred_sp_sm
+ # relu genus
+ if float(score_pred_gen_relu) >= 0.7:
+ final_decision = name_pred_gen_relu
+ # sm genus
+ if (
+ float(score_pred_gen_sm) >= 0.5
+ and name_pred_gen_sm != final_decision
+ ):
+ final_decision = name_pred_gen_sm
+ else:
+ # relu genus
+ if float(score_pred_gen_relu) >= 0.9:
+ final_decision = name_pred_gen_relu
+ # sm genus
+ if (
+ float(score_pred_gen_sm) >= 0.4
+ and name_pred_gen_sm != final_decision
+ ):
+ final_decision = name_pred_gen_sm
+ # Predicted species.
+ # Verify if genus is the same
+ else:
+ if re.search(name_pred_gen_relu, final_decision) or re.search(
+ name_pred_gen_sm, final_decision
+ ):
+ pass
+ else:
+ # relu genus
+ if float(score_pred_gen_relu) >= 0.9:
+ final_decision = name_pred_gen_relu
+ # sm genus
+ if (
+ float(score_pred_gen_sm) >= 0.5
+ and name_pred_gen_sm != final_decision
+ ):
+ final_decision = name_pred_gen_sm
+
+ # Print CSV
+ with open(input_folder + "results/results.csv", "a") as file:
+ file.write(
+ list_file_names[i]
+ + ","
+ + name_pred_gen_relu
+ + ","
+ + score_pred_gen_relu
+ + ","
+ + name_pred_gen_sm
+ + ","
+ + score_pred_gen_sm
+ + ","
+ + name_pred_sp_relu
+ + ","
+ + score_pred_sp_relu
+ + ","
+ + name_pred_sp_sm
+ + ","
+ + score_pred_sp_sm
+ + ","
+ + final_decision
+ + ","
+ + str(entropy_genus_sm[0])
+ + "\n"
+ )
+
+ # print(list_file_names[i]+","+name_pred_gen_relu+":"+score_pred_gen_relu+","+name_pred_gen_sm+":"+score_pred_gen_sm+","+name_pred_sp_relu+":"+score_pred_sp_relu+","+name_pred_sp_sm+":"+score_pred_sp_sm+","+final_decision+","+str(entropy_genus_sm))
+print(
+ '\n**Deep learning predictions have finished. Results are in file "results.csv" inside input_folder/results/.\n**Thank you for using v.HULK'
+)
diff --git a/resources/singularity/vhulk/vhulk.def b/resources/singularity/vhulk/vhulk.def
new file mode 100644
index 0000000..1314fad
--- /dev/null
+++ b/resources/singularity/vhulk/vhulk.def
@@ -0,0 +1,56 @@
+Bootstrap: docker
+From: continuumio/miniconda3
+
+%labels
+ Maintainer papanikos_182
+ Version 0.1
+ Source https://github.com/LaboratorioBioinformatica/vHULK
+ Preprint https://www.biorxiv.org/content/10.1101/2020.12.06.413476v1
+
+%files
+ vhulk_explicit.txt /opt/vHULK/
+ vHULK /opt
+ vhulk_resources.tar.gz /opt/vHULK
+
+
+%environment
+ export PATH=/opt/vHULK:$PATH
+
+%post
+ apt update && apt upgrade -y
+ conda update -y conda
+
+ conda create -n vhulk --file=/opt/vHULK/vhulk_explicit.txt
+
+ conda clean -ya
+
+ echo ". /opt/conda/etc/profile.d/conda.sh" >> $SINGULARITY_ENVIRONMENT
+ echo "conda activate vhulk" >> $SINGULARITY_ENVIRONMENT
+ tar -xvzf /opt/vHULK/vhulk_resources.tar.gz -C /opt/vHULK && rm /opt/vHULK/vhulk_resources.tar.gz
+
+%help
+ A container for vHULK v0.1 ( https://github.com/LaboratorioBioinformatica/vHULK ).
+
+ Required source scripts. models and data are stored in /opt/vHULK .
+
+ The main vHULK-v0.1.py has been modified with
+ - Portable shebang
+ - All hardcoded paths are now hardcoded for this container
+
+ To run the help menu for vHULK from this container execute
+
+ $ singularity exec library://papanikos_182/vhulk:0.1 python vHULK-v0.1.py --help
+
+ vHULK takes an input directory with one or more fasta files that are assumed to
+ be bins. It makes predictions based on its models for all bins separately.
+ That is, if you have assembled contigs you need to split them into separate files
+ in a directory and provide that as input.
+ It outputs a dir named `results`, stored within the input dir (nobody knows why..).
+ Its major output is a `results.csv` file with host predictions for each genome.
+ The results dir also contains hmmscan results and prokka annotations for all input
+ genomes/bins.
+
+ To run an anlysis for all genomes stored in the /path/to/genomes, with 8 threads
+
+ $ singularity exec library://papanikos_182/default/vhulk:0.1 \
+ python vHULK_v0.1.py -i /path/to/genomes -t 8
diff --git a/resources/singularity/vhulk/vhulk_explicit.txt b/resources/singularity/vhulk/vhulk_explicit.txt
new file mode 100644
index 0000000..ba34f2d
--- /dev/null
+++ b/resources/singularity/vhulk/vhulk_explicit.txt
@@ -0,0 +1,375 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: linux-64
+@EXPLICIT
+https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
+https://repo.anaconda.com/pkgs/main/linux-64/_tflow_select-2.3.0-mkl.conda
+https://repo.anaconda.com/pkgs/main/linux-64/ca-certificates-2020.12.8-h06a4308_0.conda
+https://repo.anaconda.com/pkgs/main/linux-64/ld_impl_linux-64-2.33.1-h53a641e_7.conda
+https://conda.anaconda.org/biobuilds/linux-64/libdb-6.2.32-0.tar.bz2
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diff --git a/resources/singularity/wish/README.md b/resources/singularity/wish/README.md
new file mode 100644
index 0000000..003fabf
--- /dev/null
+++ b/resources/singularity/wish/README.md
@@ -0,0 +1,32 @@
+# WIsH
+
+Available from `library://papanikos_182/default/wish:1.0`
+
+* Note that data dependencies are not included in the container.
+Models from [VirHostMatcher-Net](https://github.com/WeiliWw/VirHostMatcher-Net#downloading)
+are used
+
+## Procedure
+
+1. Build the image with the definition file
+```
+$ sudo singularity build wish.sif wish.def
+```
+
+3. [Optional] Sign the image
+```
+$ singularity sign wish.sif
+```
+
+4. Push it on the cloud
+```
+$ singulairty push wish.sif library://papanikos_182/default/wish:0.1
+```
+
+## Usage
+
+```
+$ singularity run library://papanikos_182/default/wish:1.0 \
+ WIsH -h
+```
+
diff --git a/resources/singularity/wish/wish.def b/resources/singularity/wish/wish.def
new file mode 100644
index 0000000..0e3e4cb
--- /dev/null
+++ b/resources/singularity/wish/wish.def
@@ -0,0 +1,45 @@
+Bootstrap: docker
+From: debian:latest
+
+%labels
+ Maintainer papanikos_182
+ Version 0.1
+ Source https://github.com/soedinglab/WIsH
+ Publication https://academic.oup.com/bioinformatics/article/33/19/3113/3964377
+
+
+%environment
+ export PATH=/opt/wish:$PATH
+
+%post
+ # Update stuff
+ apt update && apt upgrade -y
+
+ # Install compile tools for compiling wish
+ apt install -y build-essential cmake make git
+
+ # get source
+ git clone https://github.com/soedinglab/WIsH.git /opt/wish
+
+ # Get in there
+ cd /opt/wish
+
+ # Compile it
+ cmake . && make
+
+
+%help
+ A container for WIsH.
+
+ Source: https://github.com/soedinglab/WIsH
+
+ Models for host genomes are provided from VirHostMatcher-Net.
+
+ Example:
+ # Probably you need to bind the path/to/data/host_wish_model
+ $ singularity exec -B /path/to/data/host_wish_model:/data \
+ WIsH -c predict -m /data \
+ -g /path/to/phage/genomes/fastas \
+ -r /path/to/results \
+ -b
+
--
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