SOLiD

[jsun529]

Can corona_lite be installed on a single machine not on clusters, when I try to use the make function to install I get many errors.

[westerman]

Yes, corona lite can be installed on a single machine. It will work best on RedHat however it can be modified to run on other Linux distributions and even, in my case, Solaris.

If you need more help then perhaps you can post a couple of your error messages.

[jsun529]

SOLiD

Yes, corona lite can be installed on a single machine. It will work best on RedHat however it can be modified to run on other Linux distributions and even, in my case, Solaris.

If you need more help then perhaps you can post a couple of your error messages.

Thanks. Will do, at the same time what will be good installation directory on a single machine or it does not matter when you run make
"install PREFIX=/full/path/to/install" ?

[westerman]

The installation directory does not matter so long as you have write permission to it.

[jsun529]

Thanks, I am trying to intall in on SUsE, here is the error message I get first. Do I have to have a g++ compiler ( I have gcc and cc), if not how I can change the code somewhere or if I do how can I install the g++ compiler ?
/////////
localhost:~/Desktop/Corona_Lite_Plus_4.2.1 # make install PREFIX /root/Desktop/Corona_Lite_Plus_4.2.1/CORONA_LITE/
make -C pairing install PREFIX=
make[1]: Entering directory `/root/Desktop/Corona_Lite_Plus_4.2.1/pairing'
************* Building perl...
make -C perl
make[2]: Entering directory `/root/Desktop/Corona_Lite_Plus_4.2.1/pairing/perl'
make[2]: Leaving directory `/root/Desktop/Corona_Lite_Plus_4.2.1/pairing/perl'
make -C perl install
make[2]: Entering directory `/root/Desktop/Corona_Lite_Plus_4.2.1/pairing/perl'
Installing /root/Program/lib/perl/nr_mates.pl
Installing /root/Program/lib/perl/select_non_redundant_paired_tags.pl
Installing /root/Program/lib/perl/pairingDistToCounts.pl
Installing /root/Program/lib/perl/non_redundant_mates_multiple_runs_same_library.pl
Installing /root/Program/lib/perl/pairing_counts.pl
Installing /root/Program/lib/perl/combPairingHist.pl
Installing /root/Program/lib/perl/multi_chr_pairing_parser.pl
Installing /root/Program/lib/perl/mates_to_coverage_large_reference.pl
Installing /root/Program/lib/perl/pairing_by_panel.pl
Installing /root/Program/lib/perl/sizestat.pl
Installing /root/Program/lib/perl/pairing_by_group.pl
Installing /root/Program/lib/perl/gnuplotscript.pl
Installing /root/Program/lib/perl/pairing_rate_calculate.pl
Installing /root/Program/lib/perl/select_unique_paired_tags_2.pl
Installing /root/Program/lib/perl/concatenate_pairingToMates.pl
Writing /root/Program/lib/perl/x86_64-linux-thread-multi/auto/pairing/.packlist
Appending installation info to /root/Program/lib/perl/x86_64-linux-thread-multi/perllocal.pod
DESTDIR:
PREFIX:
make[2]: Leaving directory `/root/Desktop/Corona_Lite_Plus_4.2.1/pairing/perl'
install -m 755 python/*.py /bin
make[1]: Leaving directory `/root/Desktop/Corona_Lite_Plus_4.2.1/pairing'
make -C readsmap install PREFIX=
make[1]: Entering directory `/root/Desktop/Corona_Lite_Plus_4.2.1/readsmap'
cd readsmap && make map
make[2]: Entering directory `/root/Desktop/Corona_Lite_Plus_4.2.1/readsmap/readsmap'
g++ -g -O2 -march=nocona -pipe -ffast-math -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -c src/map.cxx
make[2]: g++: Command not found
make[2]: *** [map.o] Error 127
make[2]: Leaving directory `/root/Desktop/Corona_Lite_Plus_4.2.1/readsmap/readsmap'
make[1]: *** [map] Error 2
make[1]: Leaving directory `/root/Desktop/Corona_Lite_Plus_4.2.1/readsmap'
make: *** [readsmap-install] Error 2

Thanks a lot.

[jsun529]

SOLiD

Also When I try to install on my new mac, intel based, unix terminal, I got this :///

dhcp-100220:Corona_Lite_Plus_4.2.1 jessicasun$ sudo make install /Users/jessicasun/Desktop/Corona_Lite_Plus_4.2.1/CORONA_LITE
make -C pairing install PREFIX=
************* Building perl...
make -C perl
make -C perl install
Installing /share/man/man1/multi_chr_pairing_parser.pl.1
Installing /share/man/man1/nr_mates.pl.1
Installing /share/man/man1/pairing_by_group.pl.1
Installing /share/man/man1/pairing_by_panel.pl.1
Installing /share/man/man1/select_non_redundant_paired_tags.pl.1
Installing /share/man/man3/mates_to_coverage_large_reference.3pm
Installing /share/man/man3/multi_chr_pairing_parser.3pm
Installing /share/man/man3/non_redundant_mates_multiple_runs_same_library.3pm
Installing /share/man/man3/nr_mates.3pm
Installing /share/man/man3/pairing_by_group.3pm
Installing /share/man/man3/pairing_by_panel.3pm
Installing /share/man/man3/pairing_rate_calculate.3pm
Installing /share/man/man3/select_non_redundant_paired_tags.3pm
Installing /usr/bin/combPairingHist.pl
Installing /usr/bin/concatenate_pairingToMates.pl
Installing /usr/bin/gnuplotscript.pl
Installing /usr/bin/multi_chr_pairing_parser.pl
Installing /usr/bin/nr_mates.pl
Installing /usr/bin/pairing_by_group.pl
Installing /usr/bin/pairing_by_panel.pl
Installing /usr/bin/pairing_counts.pl
Installing /usr/bin/pairingDistToCounts.pl
Installing /usr/bin/select_non_redundant_paired_tags.pl
Installing /usr/bin/select_unique_paired_tags_2.pl
Installing /usr/bin/sizestat.pl
Writing /good/install/location/lib/perl/darwin-thread-multi-2level/auto/pairing/.packlist
Appending installation info to /good/install/location/lib/perl/darwin-thread-multi-2level/perllocal.pod
DESTDIR:
PREFIX:
install -m 755 python/*.py /bin
make -C readsmap install PREFIX=
cd readsmap && make map
make[2]: `map' is up to date.
cd readsmap && make mapreads
make[2]: `mapreads' is up to date.
cd readsmap && make merge_map
make[2]: `merge_map' is up to date.
cd readsmap && make mpindel_parse
make[2]: `mpindel_parse' is up to date.
cd readsmap && make pairing
make[2]: `pairing' is up to date.
cd readsmap && make panelGrouping
make[2]: `panelGrouping' is up to date.
cd readsmap && make remduphits
make[2]: `remduphits' is up to date.
cd readsmap && make rescue
make[2]: `rescue' is up to date.
install -d -m 775 /bin
cd readsmap && install -m 775 map mapreads merge_map mpindel_parse pairing panelGrouping remduphits rescue /bin/
cd readsmap && make install_schemas
g++ -g -O2 -march=nocona -pipe -ffast-math -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE src/buildschemaDB.cxx zutil.o util.o -o ./buildschemaDB
cd schemas && (ls schema_[0-9]* > lst)
cd schemas && ../buildschemaDB lst > DBschema
install -d -m 775 /etc/schemas/
install -m 444 schemas/design_to_schema_mapreads.pl schemas/k_best_schema_25_2 schemas/k_best_schema_25_2_15 schemas/k_best_schema_25_2_adj schemas/k_best_schema_25_2_adj_15 schemas/k_best_schema_25_2_adj_15_15 schemas/schema_100_0 schemas/schema_100_10 schemas/schema_100_15 schemas/schema_10_0 schemas/schema_10_1 schemas/schema_11_1 schemas/schema_12_1 schemas/schema_12_4 schemas/schema_13_0 schemas/schema_13_1 schemas/schema_14_0 schemas/schema_14_1 schemas/schema_14_2 schemas/schema_15_0 schemas/schema_15_1 schemas/schema_15_2 schemas/schema_15_3 schemas/schema_16_0 schemas/schema_16_1 schemas/schema_16_2 schemas/schema_16_3 schemas/schema_17_0 schemas/schema_17_1 schemas/schema_17_2 schemas/schema_17_3 schemas/schema_18_0 schemas/schema_18_1 schemas/schema_18_2 schemas/schema_18_3 schemas/schema_19_0 schemas/schema_19_1 schemas/schema_19_2 schemas/schema_19_3 schemas/schema_20_0 schemas/schema_20_1 schemas/schema_20_2 schemas/schema_20_3 schemas/schema_20_4 schemas/schema_20_5 schemas/schema_21_0 schemas/schema_21_1 schemas/schema_21_2 schemas/schema_21_2_adj schemas/schema_21_3 schemas/schema_22_0 schemas/schema_22_1 schemas/schema_22_2 schemas/schema_22_2_adj schemas/schema_22_3 schemas/schema_23_0 schemas/schema_23_1 schemas/schema_23_2 schemas/schema_23_2_adj schemas/schema_23_3 schemas/schema_24_0 schemas/schema_24_1 schemas/schema_24_2 schemas/schema_24_2_adj schemas/schema_24_3 schemas/schema_25_0 schemas/schema_25_1 schemas/schema_25_1_adj schemas/schema_25_2 schemas/schema_25_2_adj schemas/schema_25_2_adj_15 schemas/schema_25_2_test schemas/schema_25_3 schemas/schema_25_4 schemas/schema_25_5 schemas/schema_25_6 schemas/schema_26_0 schemas/schema_26_1 schemas/schema_26_2 schemas/schema_26_2_adj schemas/schema_26_3 schemas/schema_27_0 schemas/schema_27_1 schemas/schema_27_2 schemas/schema_27_2_adj schemas/schema_27_3 schemas/schema_28_0 schemas/schema_28_1 schemas/schema_28_2 schemas/schema_28_3 schemas/schema_28_4 schemas/schema_29_1 schemas/schema_29_2 schemas/schema_29_2_adj schemas/schema_30_0 schemas/schema_30_1 schemas/schema_30_2 schemas/schema_30_2_adj schemas/schema_30_3 schemas/schema_30_4 schemas/schema_30_5 schemas/schema_30_6 schemas/schema_30_7 schemas/schema_30_8 schemas/schema_31_2_adj schemas/schema_31_4 schemas/schema_32_1 schemas/schema_32_2_adj schemas/schema_32_3 schemas/schema_32_4 schemas/schema_32_5 schemas/schema_33_0 schemas/schema_33_1 schemas/schema_33_2_adj schemas/schema_33_3 schemas/schema_33_3_adj schemas/schema_33_4 schemas/schema_34_0 schemas/schema_34_1 schemas/schema_34_2_adj schemas/schema_34_3 schemas/schema_34_3_adj schemas/schema_34_4 schemas/schema_35_0 schemas/schema_35_1 schemas/schema_35_2 schemas/schema_35_2_adj schemas/schema_35_3 schemas/schema_35_3_adj schemas/schema_35_4 schemas/schema_35_4_adj schemas/schema_35_5 schemas/schema_35_6 schemas/schema_35_7 schemas/schema_35_8 schemas/schema_36_0 schemas/schema_36_2 schemas/schema_36_2_adj schemas/schema_36_3 schemas/schema_36_3_adj schemas/schema_36_4 schemas/schema_37_0 schemas/schema_37_2_adj schemas/schema_37_3 schemas/schema_37_3_adj schemas/schema_37_4 schemas/schema_38_0 schemas/schema_38_1 schemas/schema_38_2_adj schemas/schema_38_3_adj schemas/schema_38_4 schemas/schema_38_6 schemas/schema_39_0 schemas/schema_39_1 schemas/schema_39_2_adj schemas/schema_39_3_adj schemas/schema_39_4 schemas/schema_40_0 schemas/schema_40_1 schemas/schema_40_10 schemas/schema_40_2 schemas/schema_40_2_adj schemas/schema_40_3 schemas/schema_40_3_adj schemas/schema_40_4 schemas/schema_40_5 schemas/schema_40_6 schemas/schema_40_7 schemas/schema_40_8 schemas/schema_41_2_adj schemas/schema_41_3 schemas/schema_41_3_adj schemas/schema_41_4_adj schemas/schema_42_2_adj schemas/schema_42_3_adj schemas/schema_42_4_adj schemas/schema_43_0 schemas/schema_43_1 schemas/schema_43_2_adj schemas/schema_43_3_adj schemas/schema_43_4_adj schemas/schema_44_0 schemas/schema_44_1 schemas/schema_44_2_adj schemas/schema_44_3 schemas/schema_44_3_adj schemas/schema_44_4 schemas/schema_44_4_adj schemas/schema_44_5 schemas/schema_44_6 schemas/schema_45_0 schemas/schema_45_1 schemas/schema_45_2 schemas/schema_45_2_adj schemas/schema_45_3 schemas/schema_45_3_adj schemas/schema_45_4 schemas/schema_45_4_adj schemas/schema_45_5 schemas/schema_45_6 schemas/schema_46_2_adj schemas/schema_46_3_adj schemas/schema_46_4 schemas/schema_46_4_adj schemas/schema_47_2_adj schemas/schema_47_3_adj schemas/schema_47_4_adj schemas/schema_47_5 schemas/schema_48_0 schemas/schema_48_1 schemas/schema_48_2_adj schemas/schema_48_3_adj schemas/schema_48_4_adj schemas/schema_49_0 schemas/schema_49_1 schemas/schema_49_2_adj schemas/schema_49_3_adj schemas/schema_49_4_adj schemas/schema_49_6 schemas/schema_50_0 schemas/schema_50_1 schemas/schema_50_2 schemas/schema_50_2_adj schemas/schema_50_3 schemas/schema_50_3_adj schemas/schema_50_4 schemas/schema_50_4_adj schemas/schema_50_5 schemas/schema_50_5_adj schemas/schema_50_6 schemas/schema_50_6_adj schemas/schema_50_7 schemas/schema_55_0 schemas/schema_55_1 schemas/schema_55_2 schemas/schema_55_2_adj schemas/schema_55_3 schemas/schema_55_3_adj schemas/schema_55_4 schemas/schema_55_5 schemas/schema_55_5_adj schemas/schema_55_6 schemas/schema_56_0 schemas/schema_56_5 schemas/schema_57_5 schemas/schema_60_0 schemas/schema_60_1 schemas/schema_60_2 schemas/schema_60_3 schemas/schema_60_3_adj schemas/schema_60_4 schemas/schema_60_5 schemas/schema_60_5_adj schemas/schema_60_6 schemas/schema_65_0 schemas/schema_65_1 schemas/schema_65_2 schemas/schema_65_3 schemas/schema_65_4 schemas/schema_65_5 schemas/schema_65_6 schemas/schema_65_7 schemas/schema_70_0 schemas/schema_70_1 schemas/schema_70_2 schemas/schema_70_3 schemas/schema_70_4 schemas/schema_70_5 schemas/schema_70_6 schemas/schema_70_7 schemas/schema_70_8 schemas/schema_75_0 schemas/schema_75_1 schemas/schema_75_2 schemas/schema_75_2_adj schemas/schema_75_3 schemas/schema_75_4 schemas/schema_75_4_adj schemas/schema_75_5 schemas/schema_75_6 schemas/schema_75_7 schemas/schema_75_8 schemas/schema_75_9 schemas/schema_80_0 schemas/schema_80_8 schemas/schema_90_0 schemas/schema_9_1 schemas/schema_last_20_1_of_35 schemas/schema_last_20_1_of_45 schemas/schema_last_20_1_of_50 schemas/DBschema /etc/schemas/
install -m 444 schemas/DBschema /etc/schemas
install -d -m 775 /src
install -d -m 775 /src/readsmap
install -d -m 775 /src/readsmap/readsmap
install -d -m 775 /src/readsmap/readsmap/src
rm /src/readsmap/patched
rm: /src/readsmap/patched: No such file or directory
make[1]: [install_src] Error 1 (ignored)
ln -s /src/readsmap/readsmap/src /src/readsmap/patched
cp readsmap/Makefile /src/readsmap/readsmap
cp Makefile /src/readsmap
install -m 775 readsmap/src/FNdel.cxx readsmap/src/add_reads.cxx readsmap/src/checkpattern.cxx readsmap/src/comp_dbSNP.cxx readsmap/src/denovoadp.cxx readsmap/src/fasta-io.cxx readsmap/src/fasta-io.h readsmap/src/getComp.cxx readsmap/src/getComp.h readsmap/src/getreads.cxx readsmap/src/lowcov.cxx readsmap/src/makepattern.cxx readsmap/src/map.cxx readsmap/src/map.h readsmap/src/mapmain.cxx readsmap/src/mapreads.cxx readsmap/src/merge_map.cxx readsmap/src/merge_pat.cxx readsmap/src/miniassem.cxx readsmap/src/miniassem.h readsmap/src/minimain.cxx readsmap/src/mpindel_parse.cxx readsmap/src/mpindel_summ.cxx readsmap/src/mutseq.cxx readsmap/src/mytemplate.h readsmap/src/pairTags.cxx readsmap/src/pairTags.h readsmap/src/pairing.cxx readsmap/src/panelGrouping.cxx readsmap/src/radsort.cxx readsmap/src/remap.cxx readsmap/src/remduphits.cxx readsmap/src/rescue.cxx readsmap/src/rescue.h readsmap/src/rescuemain.cxx readsmap/src/seqstat.cxx readsmap/src/simu.cxx readsmap/src/simu_main.cxx readsmap/src/util.cxx readsmap/src/util.h readsmap/src/zcompress.cxx readsmap/src/zcompress.h readsmap/src/zutil.cxx readsmap/src/zutil.h readsmap/src/buildschemaDB.cxx /src/readsmap/readsmap/src
make -C etc install PREFIX=
make -C profile.d
make[2]: Nothing to be done for `build'.
make -C cmap
make[2]: Nothing to be done for `default'.
make -C profile.d install
/usr/bin/install -m 775 *.sh //etc/profile.d/
/usr/bin/install -m 775 *.csh //etc/profile.d/
make -C cmap install
***************** copying cmap files
/usr/bin/install -d -m 755 /etc/cmap/
/usr/bin/install -m 444 *.cmap /etc/cmap/
install -m 775 -d /etc/analysis
install -m 775 analysis/*.fsta /etc/analysis
install -m 775 analysis/*.Tm /etc/analysis
make -C conf install PREFIX=
install -m 775 -d /conf
install -m 775 *.*ml /conf
install -m 775 *.gmr /conf
install -m 775 *.tt /conf
make -C matching install PREFIX=
************* Building perl...
make -C perl
make -C perl install
Installing /share/apps/corona/lib/perl/color_convert.pl
Installing /share/apps/corona/lib/perl/concat_allchr_match_files.pl
Installing /share/apps/corona/lib/perl/concatenate_split_match_files.pl
Installing /share/apps/corona/lib/perl/coverage.pl
Installing /share/apps/corona/lib/perl/fasta2match.pl
Installing /share/apps/corona/lib/perl/generate_error_profile.pl
Installing /share/apps/corona/lib/perl/mask_schemas_mapreads.pl
Installing /share/apps/corona/lib/perl/match_to_coverage.pl
Installing /share/apps/corona/lib/perl/matching_large_genomes_cmap.pl
Installing /share/apps/corona/lib/perl/matching_large_genomes_cmap_save_script.pl
Installing /share/apps/corona/lib/perl/split_by_chromosome.pl
Installing /share/apps/corona/lib/perl/tags2genome_and_coverage.pl
Installing /share/apps/corona/lib/perl/tags2genome_dibase_pipeline.pl
Installing /share/man/man1/concat_allchr_match_files.pl.1
Installing /share/man/man1/matching_large_genomes_cmap_save_script.pl.1
Installing /share/man/man1/split_by_chromosome.pl.1
Installing /share/man/man1/tags2genome_and_coverage.pl.1
Installing /share/man/man3/concat_allchr_match_files.3pm
Installing /share/man/man3/match_to_coverage.3pm
Installing /share/man/man3/matching_large_genomes_cmap.3pm
Installing /share/man/man3/matching_large_genomes_cmap_save_script.3pm
Installing /share/man/man3/split_by_chromosome.3pm
Installing /share/man/man3/tags2genome_and_coverage.3pm
Installing /usr/bin/color_convert.pl
Installing /usr/bin/concat_allchr_match_files.pl
Installing /usr/bin/concatenate_split_match_files.pl
Installing /usr/bin/coverage.pl
Installing /usr/bin/fasta2match.pl
Installing /usr/bin/generate_error_profile.pl
Installing /usr/bin/mask_schemas_mapreads.pl
Installing /usr/bin/matching_large_genomes_cmap_save_script.pl
Installing /usr/bin/split_by_chromosome.pl
Installing /usr/bin/tags2genome_and_coverage.pl
Installing /usr/bin/tags2genome_dibase_pipeline.pl
Writing /share/apps/corona/lib/perl/darwin-thread-multi-2level/auto/matching/.packlist
Appending installation info to /share/apps/corona/lib/perl/darwin-thread-multi-2level/perllocal.pod
DESTDIR:
PREFIX:
make -C non-disco install PREFIX=
************* Building perl...
make -C perl
make -C perl install
Installing /share/apps/corona/lib/perl/non/concatenate_chr_seqs_cmap.pl
Installing /share/apps/corona/lib/perl/non/concatenate_matching_results_cmap.pl
Installing /share/apps/corona/lib/perl/non/matching_stats_human_fast.pl
Installing /share/apps/corona/lib/perl/non/matching_unique_and_random.pl
Installing /share/apps/corona/lib/perl/non/post_matching_by_chr_cmap_fast.pl
Installing /share/apps/corona/lib/perl/non/reference_validation.pl
Installing /share/apps/corona/lib/perl/non/split_by_chromosome_cmap.pl
Installing /share/apps/corona/lib/perl/non/start_points_from_match_file_fast.pl
Installing /share/apps/corona/lib/perl/non/submit_scripts_to_LSF.pl
Installing /share/apps/corona/lib/perl/non/submit_scripts_to_PBS.pl
Installing /share/apps/corona/lib/perl/non/submit_scripts_to_SGE.pl
Installing /share/man/man1/concatenate_matching_results_cmap.pl.1
Installing /share/man/man1/matching_stats_human_fast.pl.1
Installing /share/man/man1/post_matching_by_chr_cmap_fast.pl.1
Installing /share/man/man1/split_by_chromosome_cmap.pl.1
Installing /share/man/man3/non::concatenate_matching_results_cmap.3pm
Installing /share/man/man3/non::matching_stats_human_fast.3pm
Installing /share/man/man3/non:ost_matching_by_chr_cmap_fast.3pm
Installing /share/man/man3/non::split_by_chromosome_cmap.3pm
Installing /usr/bin/concatenate_chr_seqs_cmap.pl
Installing /usr/bin/concatenate_matching_results_cmap.pl
Installing /usr/bin/matching_stats_human_fast.pl
Installing /usr/bin/matching_unique_and_random.pl
Installing /usr/bin/post_matching_by_chr_cmap_fast.pl
Installing /usr/bin/reference_validation.pl
Installing /usr/bin/split_by_chromosome_cmap.pl
Installing /usr/bin/start_points_from_match_file_fast.pl
Installing /usr/bin/submit_scripts_to_LSF.pl
Installing /usr/bin/submit_scripts_to_PBS.pl
Installing /usr/bin/submit_scripts_to_SGE.pl
Writing /share/apps/corona/lib/perl/darwin-thread-multi-2level/auto/non/disco/.packlist
Appending installation info to /share/apps/corona/lib/perl/darwin-thread-multi-2level/perllocal.pod
DESTDIR:
PREFIX:
make -C share install PREFIX=
install -m 777 python/*.py /bin
make -C snp_finding install PREFIX=
************* Building perl...
make -C perl
make -C perl install
Installing /share/apps/corona/lib/perl/annotate_dbSNP_concordance_flat_file_not_mysql.pl
Installing /share/apps/corona/lib/perl/call_consensus.pl
Installing /share/apps/corona/lib/perl/concatenate_consensus_statistics.pl
Installing /share/apps/corona/lib/perl/concatenate_consensus_statistics_paste_and_awk.pl
Installing /share/apps/corona/lib/perl/concatenate_snp_probs.pl
Installing /share/apps/corona/lib/perl/consensus_prep.pl
Installing /share/apps/corona/lib/perl/consensus_prep_and_wrapper_cmap_save_script.pl
Installing /share/apps/corona/lib/perl/consensus_statistics.pl
Installing /share/apps/corona/lib/perl/consensus_statistics_concise.pl
Installing /share/apps/corona/lib/perl/consensus_wrapper.pl
Installing /share/apps/corona/lib/perl/consensus_wrapper_multiple_samples.pl
Installing /share/apps/corona/lib/perl/cw_multi_wrap.pl
Installing /share/apps/corona/lib/perl/cw_multi_wrap_general.pl
Installing /share/apps/corona/lib/perl/dibase_coverage_large_reference.pl
Installing /share/apps/corona/lib/perl/error_position_matrix_gff.pl
Installing /share/apps/corona/lib/perl/error_position_matrix_gff_by_change_scaled.pl
Installing /share/apps/corona/lib/perl/filter_snp_list_for_LMP_validation.pl
Installing /share/apps/corona/lib/perl/filter_snps_by_coverage.pl
Installing /share/apps/corona/lib/perl/foster_city_validation_group_format.pl
Installing /share/apps/corona/lib/perl/gff_to_bpv.pl
Installing /share/apps/corona/lib/perl/gff_to_consensus_step1.pl
Installing /share/apps/corona/lib/perl/gff_to_consensus_step2.pl
Installing /share/apps/corona/lib/perl/make_concatenated_error_files.pl
Installing /share/apps/corona/lib/perl/mergeColorVariantsRef.pl
Installing /share/apps/corona/lib/perl/mnp_calling.pl
Installing /share/apps/corona/lib/perl/mnp_calling_make_the_calls.pl
Installing /share/apps/corona/lib/perl/mnp_error_simulation.pl
Installing /share/apps/corona/lib/perl/non_redundant_mates_multiple_runs_same_library.pl
Installing /share/apps/corona/lib/perl/nova_cc_recall_SNPs_with_candidate_report.pl
Installing /share/apps/corona/lib/perl/nova_cc_wrapper.pl
Installing /share/apps/corona/lib/perl/plus_minus_filter.pl
Installing /share/apps/corona/lib/perl/QV_weights_to_snp_counts.pl
Installing /share/apps/corona/lib/perl/restrictVariants.pl
Installing /share/apps/corona/lib/perl/snp_accuracy_with_Ns.pl
Installing /share/apps/corona/lib/perl/snp_bp_consensus_sequence_with_Ns.pl
Installing /share/apps/corona/lib/perl/snp_confirmation_hets_exp.pl
Installing /share/apps/corona/lib/perl/snp_confirmation_multiple_samples.pl
Installing /share/apps/corona/lib/perl/snp_confirmation_multiple_samples_two_starts.pl
Installing /share/apps/corona/lib/perl/snp_confirmation_multiple_samples_yoruban.pl
Installing /share/apps/corona/lib/perl/snp_confirmation_strict_homozygous.pl
Installing /share/apps/corona/lib/perl/snp_confirmation_yoruban.pl
Installing /share/apps/corona/lib/perl/snp_consensus_sequence.pl
Installing /share/apps/corona/lib/perl/snp_counts.pl
Installing /share/apps/corona/lib/perl/snp_counts_with_QV_output.pl
Installing /share/apps/corona/lib/perl/snp_list.pl
Installing /share/apps/corona/lib/perl/snp_list_multiple_samples.pl
Installing /share/apps/corona/lib/perl/snp_list_sort.pl
Installing /share/apps/corona/lib/perl/snp_list_sort_multiple_samples.pl
Installing /share/apps/corona/lib/perl/snp_prob_wrapper.pl
Installing /share/apps/corona/lib/perl/snp_prob_wrapper_simple.pl
Installing /share/apps/corona/lib/perl/snp_probs.pl
Installing /share/apps/corona/lib/perl/snp_result_cleanup.pl
Installing /share/apps/corona/lib/perl/snp_validation_pipeline.pl
Installing /share/apps/corona/lib/perl/sp2_calling.pl
Installing /share/apps/corona/lib/perl/sp2_calling_step2_of_2.pl
Installing /share/apps/corona/lib/perl/spike_normal_ref_with_fake_adjacent_snps.pl
Installing /share/apps/corona/lib/perl/unaligned_compare.pl
Installing /share/man/man1/consensus_prep_and_wrapper_cmap_save_script.pl.1
Installing /share/man/man1/cw_multi_wrap_general.pl.1
Installing /share/man/man1/QV_weights_to_snp_counts.pl.1
Installing /share/man/man1/snp_counts.pl.1
Installing /share/man/man1/snp_counts_with_QV_output.pl.1
Installing /share/man/man3/annotate_dbSNP_concordance_flat_file_not_mysql.3pm
Installing /share/man/man3/concatenate_consensus_statistics_paste_and_awk.3pm
Installing /share/man/man3/consensus_prep_and_wrapper_cmap_save_script.3pm
Installing /share/man/man3/cw_multi_wrap_general.3pm
Installing /share/man/man3/dibase_coverage_large_reference.3pm
Installing /share/man/man3/gff_to_bpv.3pm
Installing /share/man/man3/gff_to_consensus_step1.3pm
Installing /share/man/man3/gff_to_consensus_step2.3pm
Installing /share/man/man3/make_concatenated_error_files.3pm
Installing /share/man/man3/mnp_calling.3pm
Installing /share/man/man3/mnp_calling_make_the_calls.3pm
Installing /share/man/man3/nova_cc_recall_SNPs_with_candidate_report.3pm
Installing /share/man/man3/nova_cc_wrapper.3pm
Installing /share/man/man3/QV_weights_to_snp_counts.3pm
Installing /share/man/man3/snp_counts.3pm
Installing /share/man/man3/snp_counts_with_QV_output.3pm
Installing /share/man/man3/snp_prob_wrapper.3pm
Installing /share/man/man3/snp_prob_wrapper_simple.3pm
Installing /share/man/man3/snp_validation_pipeline.3pm
Installing /share/man/man3/sp2_calling.3pm
Installing /share/man/man3/sp2_calling_step2_of_2.3pm
Installing /share/man/man3/spike_normal_ref_with_fake_adjacent_snps.3pm
Installing /usr/bin/call_consensus.pl
Installing /usr/bin/concatenate_consensus_statistics.pl
Installing /usr/bin/concatenate_snp_probs.pl
Installing /usr/bin/consensus_prep.pl
Installing /usr/bin/consensus_prep_and_wrapper_cmap_save_script.pl
Installing /usr/bin/consensus_statistics.pl
Installing /usr/bin/consensus_statistics_concise.pl
Installing /usr/bin/consensus_wrapper.pl
Installing /usr/bin/consensus_wrapper_multiple_samples.pl
Installing /usr/bin/cw_multi_wrap.pl
Installing /usr/bin/cw_multi_wrap_general.pl
Installing /usr/bin/error_position_matrix_gff.pl
Installing /usr/bin/error_position_matrix_gff_by_change_scaled.pl
Installing /usr/bin/mergeColorVariantsRef.pl
Installing /usr/bin/QV_weights_to_snp_counts.pl
Installing /usr/bin/restrictVariants.pl
Installing /usr/bin/snp_accuracy_with_Ns.pl
Installing /usr/bin/snp_bp_consensus_sequence_with_Ns.pl
Installing /usr/bin/snp_confirmation_hets_exp.pl
Installing /usr/bin/snp_confirmation_multiple_samples.pl
Installing /usr/bin/snp_confirmation_multiple_samples_two_starts.pl
Installing /usr/bin/snp_confirmation_multiple_samples_yoruban.pl
Installing /usr/bin/snp_confirmation_strict_homozygous.pl
Installing /usr/bin/snp_confirmation_yoruban.pl
Installing /usr/bin/snp_consensus_sequence.pl
Installing /usr/bin/snp_counts.pl
Installing /usr/bin/snp_counts_with_QV_output.pl
Installing /usr/bin/snp_list.pl
Installing /usr/bin/snp_list_multiple_samples.pl
Installing /usr/bin/snp_list_sort.pl
Installing /usr/bin/snp_list_sort_multiple_samples.pl
Installing /usr/bin/snp_probs.pl
Installing /usr/bin/snp_result_cleanup.pl
Installing /usr/bin/unaligned_compare.pl
Writing /share/apps/corona/lib/perl/darwin-thread-multi-2level/auto/snp_finding/.packlist
Appending installation info to /share/apps/corona/lib/perl/darwin-thread-multi-2level/perllocal.pod
DESTDIR:
PREFIX:
install -m 755 python/*.py /bin
make -C lib install PREFIX=
install -m 755 -d /lib/perl
cp --parents perl/Nova/RefLocator.pm perl/Nova/Config.pm perl/Nova/Config/Parameter.pm perl/Nova/Test/Executable.pm perl/Nova/Test/Executor.pm perl/Nova/CsfastaProcessing.pm perl/tags2genome_dibase_add_pairing_subroutines.pm perl/sequence_bias_subroutines.pm perl/tags2genome_dibase_all_color_subroutines.pm perl/parameter_util.pm perl/color_space_consensus_gff_subroutines.pm perl/find_snps_reorganized_subroutines.pm perl/PBSJob.pm perl/find_snps_by_position_subroutines_devel.pm perl/file_handling.pm perl/find_snps_subroutines.pm perl/tags2genome_dibase_lite_all_color_subroutines.pm perl/tags2genome_dibase_lite_all_color_paired_tags_subroutines.pm perl/color_space_consensus_subroutines.pm perl/paired_tags_stats_subroutines.pm perl/find_snps_by_position_subroutines.pm perl/SOLiDNova_Logging.pm perl/dna_subroutines.pm perl/tags2genome_dibase_pipeline_subroutines.pm perl/select_unique_paired_tags_subroutines.pm perl/consensus_statistics_subroutines_devel.pm perl/QueueJob.pm perl/find_single_errors_subroutines.pm perl/ReadFilter.pm perl/working_subroutines.pm perl/tags2genome_dibase_subroutines.pm perl/paired_tags_subroutines.pm perl/Queue.pm perl/consensus_statistics_subroutines.pm perl/snp_counts_subroutines.pm perl/matching_schemas.pm perl/tags2genome_dibase_lite_subroutines.pm perl/Compute/Job.pm perl/Compute/JobList.pm /lib
cp: illegal option -- -
usage: cp [-R [-H | -L | -P]] [-fi | -n] [-pvX] source_file target_file
cp [-R [-H | -L | -P]] [-fi | -n] [-pvX] source_file ... target_directory
make[1]: *** [perl] Error 64
make: *** [lib-install] Error 2
///

not sure if it will work on mac ? Thanks a lot

[westerman]

1) Yes, you need g++. This is just gnu c++ in disguise. Since you already have gcc (which is gnu 'c') I am surprised that you do not also have g++. It is possible that the alias between g++ and c++ has been lost. But if you do need g++/c++ then you should get it from the SUSE repositories or directly from gnu.org.

2) For your Mac, I can't say 100% that corona lite will run on a Mac or not. However I do run corona lite on Solaris which is probably as unlike Linux as the MacOS is. So I suspect that running on a Mac is possible. In your particular case you are missing gnu 'cp' with its '--parent' option. The solution is to install gnu 'cp' and use that. On the bright side your Mac got through the 'g++' problem.

[jsun529]

SOLiD

Dear Westerman,

Super. I have fixed the g++/c++ issues. The installation goes well until this error came along :////

Writing /root/Desktop/Corona_Lite_Plus_4.2.1/CORONA_LITE/lib/perl/x86_64-linux-thread-multi/auto/snp_finding/.packlist
Appending installation info to /root/Desktop/Corona_Lite_Plus_4.2.1/CORONA_LITE/lib/perl/x86_64-linux-thread-multi/perllocal.pod
DESTDIR:
PREFIX: /root/Desktop/Corona_Lite_Plus_4.2.1/CORONA_LITE/
make[2]: Leaving directory `/root/Desktop/Corona_Lite_Plus_4.2.1/snp_finding/perl'
install -m 755 python/*.py /root/Desktop/Corona_Lite_Plus_4.2.1/CORONA_LITE//bin
make[1]: Leaving directory `/root/Desktop/Corona_Lite_Plus_4.2.1/snp_finding'
make -C lib install PREFIX=/root/Desktop/Corona_Lite_Plus_4.2.1/CORONA_LITE/
make[1]: Entering directory `/root/Desktop/Corona_Lite_Plus_4.2.1/lib'
install -m 755 -d /root/Desktop/Corona_Lite_Plus_4.2.1/CORONA_LITE//lib/perl
cp --parents perl/Nova/RefLocator.pm perl/Nova/Config.pm perl/Nova/Config/Parameter.pm perl/Nova/Test/Executable.pm perl/Nova/Test/Executor.pm perl/Nova/CsfastaProcessing.pm perl/tags2genome_dibase_add_pairing_subroutines.pm perl/sequence_bias_subroutines.pm perl/tags2genome_dibase_all_color_subroutines.pm perl/parameter_util.pm perl/color_space_consensus_gff_subroutines.pm perl/find_snps_reorganized_subroutines.pm perl/PBSJob.pm perl/find_snps_by_position_subroutines_devel.pm perl/file_handling.pm perl/find_snps_subroutines.pm perl/tags2genome_dibase_lite_all_color_subroutines.pm perl/tags2genome_dibase_lite_all_color_paired_tags_subroutines.pm perl/color_space_consensus_subroutines.pm perl/paired_tags_stats_subroutines.pm perl/find_snps_by_position_subroutines.pm perl/SOLiDNova_Logging.pm perl/dna_subroutines.pm perl/tags2genome_dibase_pipeline_subroutines.pm perl/select_unique_paired_tags_subroutines.pm perl/consensus_statistics_subroutines_devel.pm perl/QueueJob.pm perl/find_single_errors_subroutines.pm perl/ReadFilter.pm perl/working_subroutines.pm perl/tags2genome_dibase_subroutines.pm perl/paired_tags_subroutines.pm perl/Queue.pm perl/consensus_statistics_subroutines.pm perl/snp_counts_subroutines.pm perl/matching_schemas.pm perl/tags2genome_dibase_lite_subroutines.pm perl/Compute/Job.pm perl/Compute/JobList.pm /root/Desktop/Corona_Lite_Plus_4.2.1/CORONA_LITE//lib
install -m 755 -d /root/Desktop/Corona_Lite_Plus_4.2.1/CORONA_LITE//lib/perl
cd perl-external && cp -r * /root/Desktop/Corona_Lite_Plus_4.2.1/CORONA_LITE//lib/perl
install -m 755 -d /root/Desktop/Corona_Lite_Plus_4.2.1/CORONA_LITE//lib/perl
cd perl-external-mod && cp -r * /root/Desktop/Corona_Lite_Plus_4.2.1/CORONA_LITE//lib/perl
make -C python install
make[2]: Entering directory `/root/Desktop/Corona_Lite_Plus_4.2.1/lib/python'
python ./setup.py install --prefix=/root/Desktop/Corona_Lite_Plus_4.2.1/CORONA_LITE/ --install-lib=/root/Desktop/Corona_Lite_Plus_4.2.1/CORONA_LITE//lib/python
Traceback (most recent call last):
File "./setup.py", line 3, in ?
from distutils.core import setup
ImportError: No module named distutils.core
make[2]: *** [install] Error 1
make[2]: Leaving directory `/root/Desktop/Corona_Lite_Plus_4.2.1/lib/python'
make[1]: *** [python] Error 2
make[1]: Leaving directory `/root/Desktop/Corona_Lite_Plus_4.2.1/lib'
make: *** [lib-install] Error 2

////
seems I did not have the module in python? Thanks,

[tg]

Hi,
I need to install Corona Lite on a Mac server, for trial when i tried installing it on my MacBook as root i came across 2 errors after running the make INSTALL command. The first was a pairing error and another error was
make[1]: *** [perl] Error 64.
How do i ensure whether the installation was successful or not on the MacBook and in case i want to uninstall it will running the "make clean" command be sufficient.

Should i proceed installing Corona Lite on the server if i am getting this error??

[westerman]

Should i proceed installing Corona Lite on the server if i am getting this error??

I would. You can always uninstall it. But 'make clean' is not sufficient to uninstall. Rather just remove the corona lite directory. Corona lite does not modify any system files. You can install it without being root if you want to make sure that you are not touching any vital files.

As for testing there is an e.coli test data set that you can use.

[tg]

Hi...I tried installing Corona Lite on Mac server using the same make install command and it gave me the following output with two errors at the end:


$ make install PREFIX=/Volumes/ServerHD/Corona_Lite_4.2.2

make -C pairing install PREFIX=/Volumes/ServerHD/Corona_Lite_4.2.2
************* Building perl...
make -C perl
make -C perl install
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/lib/perl/combPairingHist.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/lib/perl/concatenate_pairingToMates.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/lib/perl/gnuplotscript.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/lib/perl/mates_to_coverage_large_reference.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/lib/perl/multi_chr_pairing_parser.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/lib/perl/non_redundant_mates_multiple_runs_same_library.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/lib/perl/nr_mates.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/lib/perl/pairing_by_group.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/lib/perl/pairing_by_panel.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/lib/perl/pairing_counts.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/lib/perl/pairing_rate_calculate.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/lib/perl/pairingDistToCounts.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/lib/perl/select_non_redundant_paired_tags.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/lib/perl/select_unique_paired_tags_2.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/lib/perl/sizestat.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/share/man/man1/multi_chr_pairing_parser.pl.1
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/share/man/man1/nr_mates.pl.1
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/share/man/man1/pairing_by_group.pl.1
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/share/man/man1/pairing_by_panel.pl.1
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/share/man/man1/select_non_redundant_paired_tags.pl.1
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/share/man/man3/mates_to_coverage_large_reference.3pm
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/share/man/man3/multi_chr_pairing_parser.3pm
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/share/man/man3/non_redundant_mates_multiple_runs_same_library.3pm
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/share/man/man3/nr_mates.3pm
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/share/man/man3/pairing_by_group.3pm
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/share/man/man3/pairing_by_panel.3pm
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/share/man/man3/pairing_rate_calculate.3pm
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/share/man/man3/select_non_redundant_paired_tags.3pm
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/usr/bin/combPairingHist.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/usr/bin/concatenate_pairingToMates.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/usr/bin/gnuplotscript.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/usr/bin/multi_chr_pairing_parser.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/usr/bin/nr_mates.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/usr/bin/pairing_by_group.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/usr/bin/pairing_by_panel.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/usr/bin/pairing_counts.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/usr/bin/pairingDistToCounts.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/usr/bin/select_non_redundant_paired_tags.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/usr/bin/select_unique_paired_tags_2.pl
Installing /Volumes/ServerHD/Corona_Lite_4.2.2/usr/bin/sizestat.pl
Writing /Volumes/ServerHD/Corona_Lite_4.2.2/lib/perl/darwin-thread-multi-2level/auto/pairing/.packlist
Appending installation info to /Volumes/ServerHD/Corona_Lite_4.2.2/lib/perl/darwin-thread-multi-2level/perllocal.pod
DESTDIR:
PREFIX: /Volumes/ServerHD/Corona_Lite_4.2.2
install -m 755 python/*.py /Volumes/ServerHD/Corona_Lite_4.2.2/bin
usage: install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode]
[-o owner] file1 file2
install [-bCcpSsv] [-B suffix] [-f flags] [-g group] [-m mode]
[-o owner] file1 ... fileN directory
install -d [-v] [-g group] [-m mode] [-o owner] directory ...
make[1]: *** [install] Error 64
make: *** [pairing-install] Error 2


I need to know how significant are these errors to the correct working of Corona Lite?? Will it not run on mac and i ultimately will have to install it on Linux only??

Secondly i need your guidance in understanding that once corona lite is installed...... the files that i have is a csfasta file in gff format, and a reference sequence file in fasta format....Now to perform matching and pairing analysis how do i get/create a .cmap file, is there any perl script that i need to run or do i have to create it manually and then start performing further analysis.

Thanks in advance

[rdeborja]

Cmap

A cmap file is just a text file with the following headers:
* chromosome_ID (must be a digit)
* chromosome_name
* validated chromosome file
* double encoded chromosome file

The validated chromosome file is created using the corona lite provided reference_validation.pl script. This script changes all bases to uppercase and takes any unknown characters and converts them to N's. The double encoded reference files are generated using the corona lite provided encodeFasta.py script.

The SOLiD corona lite documentation provides examples and a bit more detail on cmap files.