最新版のインストールはまだうまくできていない 論文になっていたバージョンだと、Makefileをいじって何とかインストール可能だった
1079 cd Bridger_r2014-12-01/ 1080 ls 1081 more INSTALL 1082 ./configure --prefix=/suikou/tool/Bridger_r2014-12-01 1083 make -j 4 1084 ls 1085 ./Bridger.pl 1086 ls 1087 cd sample_test/ 1088 ls 1089 ./run_Me.sh 1090 ls 1091 nano ~/.bashrc 1092 bash 1093 su - yoshitake.kazutoshi 1094 cd .. 1095 make 1096 nano src/Makefile 1097 make 1098 cd src/ 1099 make 1100 g++ -Wall -Wno-deprecated -g -gdwarf-2 -Wunused -Wuninitialized -fpermissive -m64 -O3 -I/suikou/tool-all//include -I/suikou/tool/boost_1_56_0//include -o Assemble Assemble-utility.o Assemble-kmerhash.o Assemble-common.o Assemble-loadreads.o Assemble-splicing_graph.o Assemble-assemble.o -lboost_serialization -lboost_system -lboost_filesystem -L/suikou/tool/boost_1_56_0/lib/ 1101 make 1102 g++ -Wall -Wno-deprecated -g -gdwarf-2 -Wunused -Wuninitialized -fpermissive -m64 -O3 -I/suikou/tool-all//include -I/suikou/tool/boost_1_56_0//include -o PathSearch PathSearch-utility.o PathSearch-kmerhash.o PathSearch-common.o PathSearch-loadreads.o PathSearch-splicing_graph.o PathSearch-compatibility_graph.o PathSearch-reachability_bp_graph.o PathSearch-matching_merge.o PathSearch-path_search.o -lboost_serialization -lboost_system -lboost_filesystem -L/suikou/tool/boost_1_56_0/lib/ 1103 make 1104 nano Makefile 1105 make 1106 cd .. 1107 make 1108 nano plugins/fastool/Makefile 1109 make 1110 nano plugins/fastool/Makefile 1111 make 1112 nano plugins/fastool/Makefile 1113 make 1114 nano plugins/rsem/ 1115 nano plugins/rsem/Ma 1116 nano plugins/rsem/makefile 1117 mak 1118 make 1119 cd plugins/rsem/ 1120 make 1121 g++ -Wall -O2 -c -I. -I/suikou/tool-all/include/ parseIt.cpp 1122 make 1123 nano sam/Makefile 1124 make 1125 nano sam/misc/Makefile 1126 make 1127 g++ -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -L/suikou/tool-all/lib/ 1128 make 1129 cd sam/ 1130 make 1131 gcc -c -g -Wall -O2 -I/suikou/tool-all/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o 1132 gcc -c -g -Wall -O2 -I/suikou/tool-all/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o -I/suikou/tool/ncurses-6.0/include/ncurses/ 1133 make 1134 gcc -g -Wall -O2 -I/suikou/tool-all/include -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz -L/suikou/tool-all/lib 1135 gcc -g -Wall -O2 -I/suikou/tool-all/include -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz -L/suikou/tool/ncurses-6.0/lib/ 1136 gcc -g -Wall -O2 -I/suikou/tool-all/include -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lncurses -lm -lz -L/suikou/tool/ncurses-6.0/lib/ 1137 gcc -g -Wall -O2 -I/suikou/tool-all/include -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lncurses -lm -lz -L/suikou/tool-all/lib 1138 make 1139 gcc -g -Wall -O2 -I/suikou/tool-all/include -o samtools bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lncurses -lm -lz -L/suikou/tool-all/lib 1140 make 1141 ls 1142 nano bcftools/ 1143 make 1144 nano Makefile 1145 make 1146 nano Makefile 1147 make 1148 cd .. 1149 make 1150 cd .. 1151 make 1152 nano Makefile 1153 make 1154 ll -h plugins/rsem/makefile 1155 cd plugins/rsem/ 1156 make 1157 more makefile 1158 ll -h makefile 1159 date 1160 nano makefile 1161 make 1162 nano makefile 1163 make 1164 ll -h sam/Makefile 1165 nano sam/Makefile 1166 make 1167 nano sam/Makefile 1168 cd sam 1169 make 1170 cd .. 1171 make 1172 make -d 1173 g++ -Wall -O3 -ffast-math -c -I. EM.cpp -I/suikou/tool-all/include 1174 ls 1175 make 1176 g++ -o rsem-run-em EM.o sam/libbam.a -lz -lpthread 1177 g++ -o rsem-run-em EM.o sam/libbam.a -lz -lpthread -L/suikou/tool-all/lib 1178 make 1179 nano makefile 1180 make 1181 nano makefile 1182 make 1183 nano makefile 1184 make 1185 nano makefile 1186 make 1187 nano makefile 1188 make 1189 nano makefile 1190 make 1191 nano makefile 1192 make 1193 cd .. 1194 make 1195 ls 1196 make install 1197 ls /suikou/tool/Bridger_r2014-12-01/bin/Assemble