This page was last updated on Friday, 11-Nov-2016 11:46:02 CST

Installation notes for SOAPindel Release 2.1.4.8, 2013-02-09

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Prerequisites

svn
$ sudo apt-get install subversion

Installation

1. $ cd /programinstallers/
2. $ wget -N http://soap.genomics.org.cn/down/SOAPindel_20130209_2.1.4.8.zip
3. $ mkdir tmp
4. $ cd tmp
5. $ unzip ../SOAPindel_20130209_2.1.4.8.zip
6. $ cd indel_detection.release
7. $ make all
8. Copy README file for web page
   $ cp -puv README /U:/simonlabweb/bioinformatics/programs/soap/soapindel.README.txt
9. Install is a mess, I don't know what is important in the subdirectories, for now just do this
   $ rm *.o *.cpp *.bak Makefile
10. $ for d in v1 .DS_Store .svn draw/.svn filter/.svn fpfn/.svn simulate/.svn tools/.svn ; do rm $d -rf ; done
11. $ cp -puvr * /usr/local/bin/SOAP/
    

    `affine_align.pm' -> `/usr/local/bin/SOAP/affine_align.pm'
    `align_cluster2db_cm4.pl' -> `/usr/local/bin/SOAP/align_cluster2db_cm4.pl'
    `assemble_align' -> `/usr/local/bin/SOAP/assemble_align'
    `cluster_reads' -> `/usr/local/bin/SOAP/cluster_reads'
    `cluster_reads.pl' -> `/usr/local/bin/SOAP/cluster_reads.pl'
    `draw/view_cluster.pl' -> `/usr/local/bin/SOAP/draw/view_cluster.pl'
    `draw/draw_real_histo.pl' -> `/usr/local/bin/SOAP/draw/draw_real_histo.pl'
    `draw/draw_cmp.pl' -> `/usr/local/bin/SOAP/draw/draw_cmp.pl'
    `draw/part_align.pl' -> `/usr/local/bin/SOAP/draw/part_align.pl'
    `draw/view_fn_sim2.pl' -> `/usr/local/bin/SOAP/draw/view_fn_sim2.pl'
    `draw/draw_fxlen.pl' -> `/usr/local/bin/SOAP/draw/draw_fxlen.pl'
    `draw/draw_aligned_seq_2.pl' -> `/usr/local/bin/SOAP/draw/draw_aligned_seq_2.pl'
    `draw/view_fp_sim2.pl' -> `/usr/local/bin/SOAP/draw/view_fp_sim2.pl'
    `draw/merge_list.pl' -> `/usr/local/bin/SOAP/draw/merge_list.pl'
    `filter/merge_result.pl' -> `/usr/local/bin/SOAP/filter/merge_result.pl'
    `filter/Indel.qual.tab.x' -> `/usr/local/bin/SOAP/filter/Indel.qual.tab.x'
    `filter/filter_result_2.pl' -> `/usr/local/bin/SOAP/filter/filter_result_2.pl'
    `filter/filter_pseudo_het.pl' -> `/usr/local/bin/SOAP/filter/filter_pseudo_het.pl'
    `filter/Indel.qual.tab' -> `/usr/local/bin/SOAP/filter/Indel.qual.tab'
    `filter/filter_raw2.pl' -> `/usr/local/bin/SOAP/filter/filter_raw2.pl'
    `filter/quality_table2.pl' -> `/usr/local/bin/SOAP/filter/quality_table2.pl'
    `filter/quality_lib.pm' -> `/usr/local/bin/SOAP/filter/quality_lib.pm'
    `fpfn/merge_fpfn.pl' -> `/usr/local/bin/SOAP/fpfn/merge_fpfn.pl'
    `fpfn/indel_fmt_change.pl' -> `/usr/local/bin/SOAP/fpfn/indel_fmt_change.pl'
    `fpfn/FPFN3.pl' -> `/usr/local/bin/SOAP/fpfn/FPFN3.pl'
    `fpfn/mutPos2FPFN.pl' -> `/usr/local/bin/SOAP/fpfn/mutPos2FPFN.pl'
    `indel_detection.ibam.pl' -> `/usr/local/bin/SOAP/indel_detection.ibam.pl'
    `indel_lib.pm' -> `/usr/local/bin/SOAP/indel_lib.pm'
    `init.pl' -> `/usr/local/bin/SOAP/init.pl'
    `make_assembly_align_sh.ibam.pl' -> `/usr/local/bin/SOAP/make_assembly_align_sh.ibam.pl'
    `map_assembly_8.pl' -> `/usr/local/bin/SOAP/map_assembly_8.pl'
    `README' -> `/usr/local/bin/SOAP/README'
    `simulate/simulate_reads_gen3.pl' -> `/usr/local/bin/SOAP/simulate/simulate_reads_gen3.pl'
    `simulate/chr_mut_statistics.pl' -> `/usr/local/bin/SOAP/simulate/chr_mut_statistics.pl'
    `simulate/simulate_reads_axt_2.pl' -> `/usr/local/bin/SOAP/simulate/simulate_reads_axt_2.pl'
    `statistics_gene.pl' -> `/usr/local/bin/SOAP/statistics_gene.pl'
    `statistics.pl' -> `/usr/local/bin/SOAP/statistics.pl'
    `tools/sort.pl' -> `/usr/local/bin/SOAP/tools/sort.pl'
    `tools/sam2axtNet_p2.pl' -> `/usr/local/bin/SOAP/tools/sam2axtNet_p2.pl'
    `tools/sam2soap.pl' -> `/usr/local/bin/SOAP/tools/sam2soap.pl'
    `tools/aa_sh_index.pl' -> `/usr/local/bin/SOAP/tools/aa_sh_index.pl'
    `tools/axt2indel.pl' -> `/usr/local/bin/SOAP/tools/axt2indel.pl'
    `tools/reverseTable.pl' -> `/usr/local/bin/SOAP/tools/reverseTable.pl'
    `tools/cmp_vcf.pl' -> `/usr/local/bin/SOAP/tools/cmp_vcf.pl'
    `tools/sam2axtNet_p1.pl' -> `/usr/local/bin/SOAP/tools/sam2axtNet_p1.pl'
    `tools/aa_sh_run.pl' -> `/usr/local/bin/SOAP/tools/aa_sh_run.pl'
    `tools/list2VCF4.pl' -> `/usr/local/bin/SOAP/tools/list2VCF4.pl'
    `tools/statistics_Chimp.pl' -> `/usr/local/bin/SOAP/tools/statistics_Chimp.pl'
    `tools/run_check.pl' -> `/usr/local/bin/SOAP/tools/run_check.pl'
    `tools/dindel2list.pl' -> `/usr/local/bin/SOAP/tools/dindel2list.pl'
    `tools/run.pl' -> `/usr/local/bin/SOAP/tools/run.pl'
    `tools/GATK2list.pl' -> `/usr/local/bin/SOAP/tools/GATK2list.pl'
    `tools/pindel2list.pl' -> `/usr/local/bin/SOAP/tools/pindel2list.pl'
    `tools/sort_merge.pl' -> `/usr/local/bin/SOAP/tools/sort_merge.pl'
    `tools/run_birc.pl' -> `/usr/local/bin/SOAP/tools/run_birc.pl'
    `tools/find_tandem_repeat.pl' -> `/usr/local/bin/SOAP/tools/find_tandem_repeat.pl'
    `tools/statistics_Chimp_gene.pl' -> `/usr/local/bin/SOAP/tools/statistics_Chimp_gene.pl'
    `tools/calc_insert_size.ibam.pl' -> `/usr/local/bin/SOAP/tools/calc_insert_size.ibam.pl'

12. Cleanup
    $ cd ../..
13. $ rm tmp -rf