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comparison install_amplicon_analysis-1.3.5.sh @ 42:098ad1dd7760 draft

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planemo upload for repository https://github.com/pjbriggs/Amplicon_analysis-galaxy commit 10be6f00106e853a6720e4052871d9d84e027137
author pjbriggs
date Thu, 05 Dec 2019 11:48:01 +0000
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children 213b5cdecb70
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41:7b9786a43a16 42:098ad1dd7760
1 #!/bin/sh -e
2 #
3 # Prototype script to setup a conda environment with the
4 # dependencies needed for the Amplicon_analysis_pipeline
5 # script
6 #
7 # Handle command line
8 usage()
9 {
10 echo "Usage: $(basename $0) [DIR]"
11 echo ""
12 echo "Installs the Amplicon_analysis_pipeline package plus"
13 echo "dependencies in directory DIR (or current directory "
14 echo "if DIR not supplied)"
15 }
16 if [ ! -z "$1" ] ; then
17 # Check if help was requested
18 case "$1" in
19 --help|-h)
20 usage
21 exit 0
22 ;;
23 esac
24 # Assume it's the installation directory
25 cd $1
26 fi
27 # Versions
28 PIPELINE_VERSION=1.3.5
29 CONDA_REQUIRED_VERSION=4.6.14
30 RDP_CLASSIFIER_VERSION=2.2
31 # Directories
32 TOP_DIR=$(pwd)/Amplicon_analysis-${PIPELINE_VERSION}
33 BIN_DIR=${TOP_DIR}/bin
34 CONDA_DIR=${TOP_DIR}/conda
35 CONDA_BIN=${CONDA_DIR}/bin
36 CONDA_LIB=${CONDA_DIR}/lib
37 CONDA=${CONDA_BIN}/conda
38 ENV_NAME="amplicon_analysis_pipeline@${PIPELINE_VERSION}"
39 ENV_DIR=${CONDA_DIR}/envs/$ENV_NAME
40 #
41 # Functions
42 #
43 # Report failure and terminate script
44 fail()
45 {
46 echo ""
47 echo ERROR $@ >&2
48 echo ""
49 echo "$(basename $0): installation failed"
50 exit 1
51 }
52 #
53 # Rewrite the shebangs in the installed conda scripts
54 # to remove the full path to conda 'bin' directory
55 rewrite_conda_shebangs()
56 {
57 pattern="s,^#!${CONDA_BIN}/,#!/usr/bin/env ,g"
58 find ${CONDA_BIN} -type f -exec sed -i "$pattern" {} \;
59 }
60 #
61 # Reset conda version if required
62 reset_conda_version()
63 {
64 CONDA_VERSION="$(${CONDA_BIN}/conda -V 2>&1 | head -n 1 | cut -d' ' -f2)"
65 echo conda version: ${CONDA_VERSION}
66 if [ "${CONDA_VERSION}" != "${CONDA_REQUIRED_VERSION}" ] ; then
67 echo "Resetting conda to last known working version $CONDA_REQUIRED_VERSION"
68 ${CONDA_BIN}/conda config --set allow_conda_downgrades true
69 ${CONDA_BIN}/conda install -y conda=${CONDA_REQUIRED_VERSION}
70 else
71 echo "conda version ok"
72 fi
73 }
74 #
75 # Install conda
76 install_conda()
77 {
78 echo "++++++++++++++++"
79 echo "Installing conda"
80 echo "++++++++++++++++"
81 if [ -e ${CONDA_DIR} ] ; then
82 echo "*** $CONDA_DIR already exists ***" >&2
83 return
84 fi
85 local cwd=$(pwd)
86 local wd=$(mktemp -d)
87 cd $wd
88 wget -q https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
89 bash ./Miniconda2-latest-Linux-x86_64.sh -b -p ${CONDA_DIR}
90 echo Installed conda in ${CONDA_DIR}
91 # Reset the conda version to a known working version
92 # (to avoid problems observed with e.g. conda 4.7.10)
93 echo ""
94 reset_conda_version
95 # Update the installation files
96 # This is to avoid problems when the length the installation
97 # directory path exceeds the limit for the shebang statement
98 # in the conda files
99 echo ""
100 echo -n "Rewriting conda shebangs..."
101 rewrite_conda_shebangs
102 echo "ok"
103 echo -n "Adding conda bin to PATH..."
104 PATH=${CONDA_BIN}:$PATH
105 echo "ok"
106 cd $cwd
107 rm -rf $wd/*
108 rmdir $wd
109 }
110 #
111 # Create conda environment
112 install_conda_packages()
113 {
114 echo "+++++++++++++++++++++++++"
115 echo "Installing conda packages"
116 echo "+++++++++++++++++++++++++"
117 local cwd=$(pwd)
118 local wd=$(mktemp -d)
119 cd $wd
120 cat >environment.yml <<EOF
121 name: ${ENV_NAME}
122 channels:
123 - defaults
124 - conda-forge
125 - bioconda
126 dependencies:
127 - python=2.7
128 - cutadapt=1.8
129 - sickle-trim=1.33
130 - bioawk=1.0
131 - pandaseq=2.8.1
132 - spades=3.10.1
133 - fastqc=0.11.3
134 - qiime=1.9.1
135 - blast-legacy=2.2.26
136 - fasta-splitter=0.2.6
137 - rdp_classifier=$RDP_CLASSIFIER_VERSION
138 - vsearch=2.10.4
139 - r=3.5.1
140 - r-tidyverse=1.2.1
141 - bioconductor-dada2=1.8
142 - bioconductor-biomformat=1.8.0
143 EOF
144 ${CONDA} env create --name "${ENV_NAME}" -f environment.yml
145 echo Created conda environment in ${ENV_DIR}
146 cd $cwd
147 rm -rf $wd/*
148 rmdir $wd
149 #
150 # Patch qiime 1.9.1 tools to switch deprecated 'axisbg'
151 # matplotlib property to 'facecolor':
152 # https://matplotlib.org/api/prev_api_changes/api_changes_2.0.0.html
153 echo ""
154 for exe in make_2d_plots.py plot_taxa_summary.py ; do
155 echo -n "Patching ${exe}..."
156 find ${CONDA_DIR} -type f -name "$exe" -exec sed -i 's/axisbg=/facecolor=/g' {} \;
157 echo "done"
158 done
159 #
160 # Patch qiime 1.9.1 tools to switch deprecated 'set_axis_bgcolor'
161 # method call to 'set_facecolor':
162 # https://matplotlib.org/api/_as_gen/matplotlib.axes.Axes.set_axis_bgcolor.html
163 for exe in make_rarefaction_plots.py ; do
164 echo -n "Patching ${exe}..."
165 find ${CONDA_DIR} -type f -name "$exe" -exec sed -i 's/set_axis_bgcolor/set_facecolor/g' {} \;
166 echo "done"
167 done
168 }
169 #
170 # Install all the non-conda dependencies in a single
171 # function (invokes separate functions for each package)
172 install_non_conda_packages()
173 {
174 echo "+++++++++++++++++++++++++++++"
175 echo "Installing non-conda packages"
176 echo "+++++++++++++++++++++++++++++"
177 # Temporary working directory
178 local wd=$(mktemp -d)
179 local cwd=$(pwd)
180 local wd=$(mktemp -d)
181 cd $wd
182 # Amplicon analysis pipeline
183 echo -n "Installing Amplicon_analysis_pipeline..."
184 if [ -e ${BIN_DIR}/Amplicon_analysis_pipeline.sh ] ; then
185 echo "already installed"
186 else
187 install_amplicon_analysis_pipeline
188 echo "ok"
189 fi
190 # ChimeraSlayer
191 echo -n "Installing ChimeraSlayer..."
192 if [ -e ${BIN_DIR}/ChimeraSlayer.pl ] ; then
193 echo "already installed"
194 else
195 install_chimeraslayer
196 echo "ok"
197 fi
198 # Uclust
199 # This no longer seems to be available for download from
200 # drive5.com so don't download
201 echo "WARNING uclust not available: skipping installation"
202 }
203 #
204 # Amplicon analyis pipeline
205 install_amplicon_analysis_pipeline()
206 {
207 local wd=$(mktemp -d)
208 local cwd=$(pwd)
209 local wd=$(mktemp -d)
210 cd $wd
211 wget -q https://github.com/MTutino/Amplicon_analysis/archive/${PIPELINE_VERSION}.tar.gz
212 tar zxf ${PIPELINE_VERSION}.tar.gz
213 cd Amplicon_analysis-${PIPELINE_VERSION}
214 INSTALL_DIR=${TOP_DIR}/share/amplicon_analysis_pipeline-${PIPELINE_VERSION}
215 mkdir -p $INSTALL_DIR
216 ln -s $INSTALL_DIR ${TOP_DIR}/share/amplicon_analysis_pipeline
217 for f in *.sh *.R ; do
218 /bin/cp $f $INSTALL_DIR
219 done
220 /bin/cp -r uc2otutab $INSTALL_DIR
221 mkdir -p ${BIN_DIR}
222 cat >${BIN_DIR}/Amplicon_analysis_pipeline.sh <<EOF
223 #!/usr/bin/env bash
224 #
225 # Point to Qiime config
226 export QIIME_CONFIG_FP=${TOP_DIR}/qiime/qiime_config
227 # Set up the RDP jar file
228 export RDP_JAR_PATH=${TOP_DIR}/share/rdp_classifier/rdp_classifier-${RDP_CLASSIFIER_VERSION}.jar
229 # Set the Matplotlib backend
230 export MPLBACKEND="agg"
231 # Put the scripts onto the PATH
232 export PATH=${BIN_DIR}:${INSTALL_DIR}:\$PATH
233 # Activate the conda environment
234 export PATH=${CONDA_BIN}:\$PATH
235 source ${CONDA_BIN}/activate ${ENV_NAME}
236 # Execute the driver script with the supplied arguments
237 $INSTALL_DIR/Amplicon_analysis_pipeline.sh \$@
238 exit \$?
239 EOF
240 chmod 0755 ${BIN_DIR}/Amplicon_analysis_pipeline.sh
241 cat >${BIN_DIR}/install_reference_data.sh <<EOF
242 #!/usr/bin/env bash -e
243 #
244 function usage() {
245 echo "Usage: \$(basename \$0) DIR"
246 }
247 if [ -z "\$1" ] ; then
248 usage
249 exit 0
250 elif [ "\$1" == "--help" ] || [ "\$1" == "-h" ] ; then
251 usage
252 echo ""
253 echo "Install reference data into DIR"
254 exit 0
255 fi
256 echo "=========================================="
257 echo "Installing Amplicon analysis pipeline data"
258 echo "=========================================="
259 if [ ! -e "\$1" ] ; then
260 echo "Making directory \$1"
261 mkdir -p \$1
262 fi
263 cd \$1
264 DATA_DIR=\$(pwd)
265 echo "Installing reference data under \$DATA_DIR"
266 $INSTALL_DIR/References.sh
267 echo ""
268 echo "Use '-r \$DATA_DIR' when running Amplicon_analysis_pipeline.sh"
269 echo "to use the reference data from this directory"
270 echo ""
271 echo "\$(basename \$0): finished"
272 EOF
273 chmod 0755 ${BIN_DIR}/install_reference_data.sh
274 cd $cwd
275 rm -rf $wd/*
276 rmdir $wd
277 }
278 #
279 # ChimeraSlayer
280 install_chimeraslayer()
281 {
282 local cwd=$(pwd)
283 local wd=$(mktemp -d)
284 cd $wd
285 wget -q https://sourceforge.net/projects/microbiomeutil/files/__OLD_VERSIONS/microbiomeutil_2010-04-29.tar.gz
286 tar zxf microbiomeutil_2010-04-29.tar.gz
287 cd microbiomeutil_2010-04-29
288 INSTALL_DIR=${TOP_DIR}/share/microbiome_chimeraslayer-2010-04-29
289 mkdir -p $INSTALL_DIR
290 ln -s $INSTALL_DIR ${TOP_DIR}/share/microbiome_chimeraslayer
291 /bin/cp -r ChimeraSlayer $INSTALL_DIR
292 cat >${BIN_DIR}/ChimeraSlayer.pl <<EOF
293 #!/usr/bin/env bash
294 export PATH=$INSTALL_DIR:\$PATH
295 $INSTALL_DIR/ChimeraSlayer/ChimeraSlayer.pl $@
296 EOF
297 chmod 0755 ${INSTALL_DIR}/ChimeraSlayer/ChimeraSlayer.pl
298 chmod 0755 ${BIN_DIR}/ChimeraSlayer.pl
299 cd $cwd
300 rm -rf $wd/*
301 rmdir $wd
302 }
303 #
304 # uclust required for QIIME/pyNAST
305 # License only allows this version to be used with those two packages
306 # See: http://drive5.com/uclust/downloads1_2_22q.html
307 install_uclust()
308 {
309 local cwd=$(pwd)
310 local wd=$(mktemp -d)
311 cd $wd
312 wget -q http://drive5.com/uclust/uclustq1.2.22_i86linux64
313 INSTALL_DIR=${TOP_DIR}/share/uclust-1.2.22
314 mkdir -p $INSTALL_DIR
315 ln -s $INSTALL_DIR ${TOP_DIR}/share/uclust
316 /bin/mv uclustq1.2.22_i86linux64 ${INSTALL_DIR}/uclust
317 chmod 0755 ${INSTALL_DIR}/uclust
318 ln -s ${INSTALL_DIR}/uclust ${BIN_DIR}
319 cd $cwd
320 rm -rf $wd/*
321 rmdir $wd
322 }
323 setup_pipeline_environment()
324 {
325 echo "+++++++++++++++++++++++++++++++"
326 echo "Setting up pipeline environment"
327 echo "+++++++++++++++++++++++++++++++"
328 # fasta_splitter.pl
329 echo -n "Setting up fasta_splitter.pl..."
330 if [ -e ${BIN_DIR}/fasta-splitter.pl ] ; then
331 echo "already exists"
332 elif [ ! -e ${ENV_DIR}/share/fasta-splitter/fasta-splitter.pl ] ; then
333 echo "failed"
334 fail "fasta-splitter.pl not found"
335 else
336 ln -s ${ENV_DIR}/share/fasta-splitter/fasta-splitter.pl ${BIN_DIR}/fasta-splitter.pl
337 echo "ok"
338 fi
339 # rdp_classifier.jar
340 local rdp_classifier_jar=rdp_classifier-${RDP_CLASSIFIER_VERSION}.jar
341 echo -n "Setting up rdp_classifier.jar..."
342 if [ -e ${TOP_DIR}/share/rdp_classifier/${rdp_classifier_jar} ] ; then
343 echo "already exists"
344 elif [ ! -e ${ENV_DIR}/share/rdp_classifier/rdp_classifier.jar ] ; then
345 echo "failed"
346 fail "rdp_classifier.jar not found"
347 else
348 mkdir -p ${TOP_DIR}/share/rdp_classifier
349 ln -s ${ENV_DIR}/share/rdp_classifier/rdp_classifier.jar ${TOP_DIR}/share/rdp_classifier/${rdp_classifier_jar}
350 echo "ok"
351 fi
352 # qiime_config
353 echo -n "Setting up qiime_config..."
354 if [ -e ${TOP_DIR}/qiime/qiime_config ] ; then
355 echo "already exists"
356 else
357 mkdir -p ${TOP_DIR}/qiime
358 cat >${TOP_DIR}/qiime/qiime_config <<EOF-qiime-config
359 qiime_scripts_dir ${ENV_DIR}/bin
360 EOF-qiime-config
361 echo "ok"
362 fi
363 }
364 #
365 # Top level script does the installation
366 echo "======================================="
367 echo "Amplicon_analysis_pipeline installation"
368 echo "======================================="
369 echo "Installing into ${TOP_DIR}"
370 if [ -e ${TOP_DIR} ] ; then
371 fail "Directory already exists"
372 fi
373 mkdir -p ${TOP_DIR}
374 install_conda
375 install_conda_packages
376 install_non_conda_packages
377 setup_pipeline_environment
378 echo "===================================="
379 echo "Amplicon_analysis_pipeline installed"
380 echo "===================================="
381 echo ""
382 echo "Install reference data using:"
383 echo ""
384 echo "\$ ${BIN_DIR}/install_reference_data.sh DIR"
385 echo ""
386 echo "Run pipeline scripts using:"
387 echo ""
388 echo "\$ ${BIN_DIR}/Amplicon_analysis_pipeline.sh ..."
389 echo ""
390 echo "(or add ${BIN_DIR} to your PATH)"
391 echo ""
392 echo "$(basename $0): finished"
393 ##
394 #