This page was last updated on Friday, 10-Mar-2023 19:33:40 CST
Installation Instructions http://repeatexplorer.umbr.cas.cz/static/html/help/manual.html#installation
Another person's installation notes
http://williams-lab.wikidot.com/repeatexplorer
=== Dependencies ==== These dependencies are assumed to have executables in path: R (v >= 2.14 r-project.org) including packages: foreach, igraph, getopt, R2HTML, lattice, doMC, multicore, ape and Biostrings (available from www.bioconductor.org) Perl and BioPerl (core) Python v. >=2.6 ImageMagick NCBI Basic Local Alignment Search Tool version 2.2.xx Muscle (not necessary for clustering fasty36 (not necessary for clustering) Included dependencies, does not require setting for command line version: GNU parallel (included ) Louvain clustering - now provided with RepeatExplorer, must be compiled from source, see 'louvain' directory TGICL - copy of tgicl was obtained from http://sourceforge.net/projects/tgicl/files/tgicl/tgicl_linux/tgicl_linux.tar.gz/download (newer version does not work with repatexplorer!) Paths to below dependencies have to be specified in config.sh: if RepeatMasker is not in path, RepeatMasker directory must be specified explicitly in config.sh Conserved domain database (only necessary when rpsblast search is included)
<!-- disable ghostscript format types --> <!-- <policy domain="coder" rights="none" pattern="PS" /> <policy domain="coder" rights="none" pattern="PS2" /> <policy domain="coder" rights="none" pattern="PS3" /> <policy domain="coder" rights="none" pattern="EPS" /> <policy domain="coder" rights="none" pattern="PDF" /> <policy domain="coder" rights="none" pattern="XPS" /> --> <policy domain="coder" rights="read|write" pattern="PDF,PS" />
GALAXY_DIR= /dev/null # this variable is not neccessary for command line version # USE ABSOLUTE PATHS # directory with RepeatMAsker installation export REPEAT_MASKER= /usr/local/bin/RepeatMasker/RepeatMasker # set according your local installation, if RepeatMasker is in path you comment the line out # Conserved domain database files :location: export RPSBLAST_DATABASE= /usr/local/bin/repeatexplorer/cdd # set according your local installation export RPSBLAST_DATABASE_ANNOTATION= /usr/local/bin/repeatexplorer/cdd/cddid.tbl # set according your local installation PATH=${ROOT}/parallel/src:$PATH export PATH export TGICL=${ROOT}/tgicl_linux # directory with louvain clustering ex e cutables: export PROG_COMMUNITY=${ROOT}/louvain # make sure that you have compiled source using make! export OGDF=${ROOT}/OGDF/runOGDFlayout export JSLIB=$ROOT/umbr_programs/interactive_graph/js # DO NOT MODIFY export DOMAINDATABASE=$ROOT/tool-data/domains/TE_domains_newest.fasta # DO NOT MODIFY! export DOMAIN_TYPES=$ROOT/tool-data/domains/classification_newest.csv # DO NOT MODIFY! export MIN_MINCL=20 #limit for minimal size of the MINCL, DO NOT MODIFY export MAXEDGES=350000000 # depends on computer memory determine maximal amount of data which could be process DO NOT MODIFY export MAXEDGES_FOR_LAYOUT=25000000 # adjusted down for fmmm layout export MAXNODES_FOR_LAYOUT=50000 export PROC_LAYOUT=4 # recommendations 16G RAM then MAXEDGES~341576829
…pipeline version: failed to get version number! This is clustering pipeline
requesting all changes adding changesets adding manifests adding file changes added 4 changesets with 11 changes to 7 files updating to branch default 6 files updated, 0 files merged, 0 files removed, 0 files unresolved
total 142780 -rw-rw-r-- 1 admin admin 156 Nov 21 10:14 README.txt -rw-rw-r-- 1 admin admin 117057027 Nov 21 10:14 dna_database.fasta -rw-rw-r-- 1 admin admin 10772 Nov 21 10:14 dna_database.fasta.nin -rw-rw-r-- 1 admin admin 102307 Nov 21 10:14 dna_database.fasta.nhr -rw-rw-r-- 1 admin admin 28903195 Nov 21 10:14 dna_database.fasta.nsq -rw-rw-r-- 1 admin admin 122733 Nov 21 10:14 dna_database_codes.csv
#!/bin/bash cd /usr/local/bin/repeatexplorer/tests rm ../test_data/test_dir/* -rf ./test1.sh &> test1.log ./test2.sh &> test2.log ./test3.sh &> test3.log ./test4.sh &> test4.log ./test5_interlacers.sh &> test5.log ./test6_interlacers.sh &> test6.log ./test7.sh &> test7.log ./test8_fastq_filtering_and_clustering.sh &> test8.log ./test9_fastq_filtering.sh &> test9.log ./test10_fastq_filtering_and_clustering_example.sh &> test10.log ./test11_gl_layouts.sh &> test11.log
10_fastq_filtering_and_clustering_example.sh.log: exit status : 0 test_test10_fastq_filtering_and_clustering_example.sh.log: exit status : 0 test_test10_fastq_filtering_and_clustering_example.sh.log: exit status : 0 test_test10_fastq_filtering_and_clustering_example.sh.log: exit status of clustering: 0 test_test11_gl_layouts.sh.log: exit status : 0 test_test1.sh.log: exit status of run1: 0 test_test1.sh.log: exit status of run2: 0 test_test2.sh.log: exit status of run1: 0 test_test2.sh.log: exit status of run2: 0 test_test3.sh.log: exit status of run1: 0 test_test3.sh.log: exit status of run2: 0 test_test4.sh.log: exit status of run7: 0 test_test4.sh.log: exit status of run8: 0 test_test4.sh.log: exit status of run9: 0 test_test5_interlacers.sh.log: exit status: 0 test_test5_interlacers.sh.log: exit status: 0 test_test5_interlacers.sh.log: exit status: 0 test_test5_interlacers.sh.log: exit status: 1 test_test5_interlacers.sh.log: exit status: 1 test_test5_interlacers.sh.log: exit status: 1 test_test6_interlacers.sh.log: exit status: 0 test_test7.sh.log: exit status of run10: 0 test_test7.sh.log: exit status of run11: 0 test_test7.sh.log: exit status of run12: 0 test_test7.sh.log:exit status:1 test_test7.sh.log: exit status of run13: 0 test_test8_fastq_filtering_and_clustering.sh.log: exit status : 0 test_test8_fastq_filtering_and_clustering.sh.log: exit status : 0 test_test8_fastq_filtering_and_clustering.sh.log: exit status : 0 test_test8_fastq_filtering_and_clustering.sh.log: exit status : 0 test_test8_fastq_filtering_and_clustering.sh.log: exit status : 0 test_test8_fastq_filtering_and_clustering.sh.log: exit status : 0 test_test8_fastq_filtering_and_clustering.sh.log: exit status of clustering: 0 test_test8_fastq_filtering_and_clustering.sh.log: exit status of merging: 0 test_test9_fastq_filtering.sh.log: exit status : 0 test_test9_fastq_filtering.sh.log: exit status : 0 test_test9_fastq_filtering.sh.log: exit status : 0 test_test9_fastq_filtering.sh.log: exit status : 0 test_test9_fastq_filtering.sh.log: exit status : 0 test_test9_fastq_filtering.sh.log: exit status : 0 test_test9_fastq_filtering.sh.log: exit status : 0 test_test9_fastq_filtering.sh.log: exit status : 0 test_test9_fastq_filtering.sh.log: exit status : 0