Removing old Bash versions of scripts replaced by new Python versions

scripts/get_sbt.sh

@@ -1,42 +0,0 @@
-#!/bin/bash
-#
-# Prepare for taxonomic classification
-# by downloading SBT (sequence bloom trees)
-# for microbial genomes in refseq and genbank.
-
-mkdir -p data/
-cd data/
-
-tar_files=( \
-"microbe-refseq-sbt-k51-2017.05.09.tar.gz"
-"microbe-refseq-sbt-k31-2017.05.09.tar.gz"
-"microbe-refseq-sbt-k21-2017.05.09.tar.gz"
-"microbe-genbank-sbt-k51-2017.05.09.tar.gz"
-"microbe-genbank-sbt-k31-2017.05.09.tar.gz"
-"microbe-genbank-sbt-k21-2017.05.09.tar.gz"
-)
-
-for tar_file in "${tar_files[@]}"
-do
-    curl -O https://s3-us-west-1.amazonaws.com/spacegraphcats.ucdavis.edu/${tar_file}
-    tar xzf ${tar_file}
-    rm -rf ${tar_file}
-done
-
-#
-# The individual signatures for the above SBTs were calculated as follows:
-# 
-# sourmash compute -k 4,5 \
-#    -n 2000 \
-#    --track-abundance \
-#    --name-from-first \
-#    -o {output} \
-#    {input}
-#
-#+sourmash compute -k 21,31,51 \
-#     --scaled 2000 \
-#     --track-abundance \
-#     --name-from-first \
-#     -o {output} \
-#     {input}
-#

scripts/install_singularity.sh

@@ -1,43 +0,0 @@
-#!/bin/bash
-#
-# Prepare the workflow for Singularity
-
-if [ "$(id -u)" != "0" ]; then
-    echo ""
-    echo ""
-    echo "This script should be run as root."
-    echo ""
-    echo ""
-    exit 1;
-fi
-
-
-# ================================
-# Install Prerequisites:
-
-# Update aptitude and install dependencies
-apt-get -y update
-
-apt-get -y install zlib1g-dev
-apt-get -y install ncurses-dev
-
-# Install Docker
-wget -qO- https://get.docker.com/ | sh
-usermod -aG docker ubuntu
-
-
-# ================================
-# Install Singularity:
-
-wget -O- http://neuro.debian.net/lists/xenial.us-ca.full | tee /etc/apt/sources.list.d/neurodebian.sources.list
-apt-key adv --recv-keys --keyserver hkp://pool.sks-keyservers.net:80 0xA5D32F012649A5A9
-apt-get update
-apt-get install -y singularity-container
-singularity --version
-
-echo ""
-echo ""
-echo "Singularity is now installed. Log out and log back in for docker group to take effect."
-echo ""
-echo ""
-

scripts/install_snakemake.sh

@@ -1,41 +0,0 @@
-#!/bin/bash
-
-if [ "$(id -u)" == "0" ]; then
-    echo ""
-    echo ""
-    echo "This script should be run as a normal user."
-    echo ""
-    echo ""
-    exit 1;
-fi
-
-
-# ================================
-# Install Snakemake:
-
-CONDA="miniconda3-4.3.30"
-
-# Use pyenv to install conda 
-pyenv install $CONDA
-
-# Set that as the distro of choice
-pyenv global $CONDA
-
-# This sets the $PATH shims so condaa is the pyenv conda
-eval "$(pyenv init -)"
-
-conda update
-conda config --add channels r
-conda config --add channels defaults
-conda config --add channels conda-forge
-conda config --add channels bioconda
-
-conda install --yes -c bioconda snakemake
-
-
-# ===============================
-# Install OSF CLI client
-
-pip install --upgrade pip
-pip install --user osfclient
-

scripts/prepare_biocontainers.sh

@@ -1,6 +0,0 @@
-#!/bin/bash
-
-docker pull quay.io/biocontainers/sourmash:2.0.0a3--py36_0
-docker pull quay.io/biocontainers/krona:2.7--pl5.22.0_1
-docker pull quay.io/biocontainers/kaiju:1.5.0--pl5.22.0_0
-

scripts/unpack_kaiju.sh

@@ -1,8 +0,0 @@
-#!/bin/bash
-
-mkdir kaijudb
-cd kaijudb
-curl -LO http://kaiju.binf.ku.dk/database/kaiju_index_nr_euk.tgz
-tar zxvf kaiju_index_nr_euk.tgz
-rm -r kaiju_index_nr_euk.tgz
-cd ../