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#!/bin/bash
# Remark: Considere running runtime test suite which is different from
# this one which is based on the docs. If this would be implemented
# we should probably ship all example data and doc in a separate
# phyx-doc package
set -e
pkg=phyx
if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi
cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}"
cd "${AUTOPKGTEST_TMP}"
cd pxaa2cdn_example && echo pxaa2cdn && pxaa2cdn -a ND6_aa.fa -n ND6_nuc.fa -o CDN_aln.fa >/dev/null && cd ..
cd pxbdfit_example && echo pxbdfit && pxbdfit -t bd.tre -m yule >/dev/null && cd ..
# cd pxbdsim_example && echo pxbdsim && pxbdsim -e 100 -s -b 1 -d 0.5 -o output_tree_file >/dev/null && cd ..
cd pxboot_example && echo pxboot && pxboot -s Alignment -x 112233 -f 0.50 -o output_of_50_jackknife >/dev/null && cd ..
cd pxboot_example && echo pxboot && pxboot -s Alignment -p parts -o output_of_bootstrap >/dev/null && cd ..
cd pxbp_example && echo pxbp && pxbp -t Tree.tre -o bp_output >/dev/null && cd ..
cd pxcat_example && echo pxcat && pxcat -s *.fas *.fa *.phy -p Parts.txt -o Supermatrix.fa >/dev/null && cd ..
cd pxclsq_example && echo pxclsq && pxclsq -s Alignment -p 0.6 >/dev/null && cd ..
cd pxconsq_example && echo pxconsq && pxconsq -s Alignment >/dev/null && cd ..
cd pxcontrates_example && echo pxcontrates && pxcontrates -c contrates_file.txt -t contrates_tree.tre -a 1 >/dev/null 2>/dev/null && cd ..
cd pxfqfilt_example && echo pxfqfilt && pxfqfilt -s fqfilt_test.fastq -m 10 >/dev/null && cd ..
cd pxlog_example && echo pxlog && pxlog -t *.trees -i >/dev/null && cd ..
cd pxlog_example && echo pxlog && pxlog -t *.trees -b 75 -n 2 -o some_output_filename >/dev/null && cd ..
cd pxlssq_example && echo pxlssq && pxlssq -s Alignment >/dev/null && cd ..
cd pxlstr_example && echo pxlstr && pxlstr -t Tree.tre >/dev/null && cd ..
cd pxmrca_example && echo pxmrca && pxmrca -t mrca_test.tre -m mrca.txt >/dev/null && cd ..
cd pxmrcacut_example && echo pxmrcacut && pxmrcacut -t mrca_test.tre -m mrca.txt >/dev/null && cd ..
cd pxmrcaname_example && echo pxmrcaname && pxmrcaname -t mrca_test.tre -m mrca.txt >/dev/null && cd ..
cd pxnj_example && echo pxnj && pxnj -s Alignment.aln >/dev/null && cd ..
cd pxnw_examples && echo pxnw && pxnw -s Alignment.aln >/dev/null && cd ..
cd pxrecode_example && echo pxrecode && pxrecode -s Nucleotide.fa >/dev/null && cd ..
cd pxrevcomp_example && echo pxrevcomp && pxrevcomp -s Nucleotide.fa >/dev/null && cd ..
cd pxrls_example && echo pxrls && pxrls -s test.fa -c oldnames.txt -n newnames.txt >/dev/null && cd ..
cd pxrlt_example && echo pxrlt && pxrlt -t kingdoms.tre -c kingdoms.oldnames.txt -n kingdoms.newnames.txt >/dev/null && cd ..
cd pxrms_example && echo pxrms && pxrms -s Nucleotide.fa -f taxa_to_delete.txt >/dev/null && cd ..
cd pxrmt_example && echo pxrmt && pxrmt -t rmt_test.tre -n s1,s6,s8 >/dev/null && cd ..
cd pxrr_example && echo pxrr && pxrr -t rr_test.tre -g s1,s2 >/dev/null && cd ..
cd pxs2fa_pxs2phy_pxs2nex_example && \
echo pxs2fa && pxs2fa -s Alignment >/dev/null && \
echo pxs2phy && pxs2phy -s Alignment >/dev/null && \
echo pxs2nex && pxs2nex -s Alignment >/dev/null && \
cd ..
cd pxseqgen_example && echo pxseqgen && pxseqgen -t seqgen_test.tre >/dev/null && cd ..
cd pxseqgen_example && echo pxseqgen && pxseqgen -t seqgen_test.tre -o output_alignment -m .33,.33,.33,.33,.33,.33,2,.3,.3,.2,.5,.4,.2 >/dev/null && cd ..
cd pxsstat_example && echo pxsstat && pxsstat -s Bollback_2002_MBE.fa >/dev/null && cd ..
cd pxstrec_example && echo pxstrec && pxstrec -d test.data.narrow -t test.tre -c config_stmap >/dev/null && cd ..
cd pxsw_example && echo pxsw && pxsw -s Alignment.fa >/dev/null && cd ..
cd pxt2new_example && echo pxt2new && pxt2new -t Tree.nex >/dev/null && cd ..
cd pxtlate_example && echo pxtlate && pxtlate -s Sequence.fa >/dev/null && cd ..
cd pxtscale_example && echo pxtscale && pxtscale -t ultra.tre -s 2.0 >/dev/null && cd ..
cd pxupgma_example && echo pxupgma && pxupgma -s drosophila.aln >/dev/null && cd ..
cd pxvcf2fa_example && echo pxvcf2fa && pxvcf2fa -s vcf_file >/dev/null && cd ..
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