STACK_1.41: fixed build process but not sure everything is configured as it should as some files seem to have changed names

Author: Raynooo

stacks/1.41/Dockerfile

@@ -32,12 +32,13 @@ RUN ln -s /usr/include/google /usr/include/sparsehash && \
     ./configure --enable-sparsehash --enable-bam --with-bam-include-path=/usr/include/samtools --with-bam-lib-path=/usr/lib && \
     make -j 8 && \
     make install && \
-    rm -rf /usr/local/share/stacks/php && \
-    sed -i -e 's,$mysql_config;,$mysql_config;\nmy $cnf_secure = $cnf . (exists $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} ? " --host=" . $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} : (exists $ENV{"MYSQL_HOST"} ? " --host=" . $ENV{"MYSQL_HOST"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} ? " --password=" . $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} : (exists $ENV{"MYSQL_PASS"} ? " --password=" . $ENV{"MYSQL_PASS"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_USER"} ? " --user=" . $ENV{"MYSQL_APP_ENV_MYSQL_USER"} : (exists $ENV{"MYSQL_USER"} ? " --user=" . $ENV{"MYSQL_USER"} : q{}));,' -i -e 's,mysql --defaults-file=$cnf,mysql --defaults-file=$cnf_secure,g' /usr/local/bin/denovo_map.pl && \
+    rm -rf /usr/local/share/stacks/php
+
+RUN sed -i -e 's,$mysql_config;,$mysql_config;\nmy $cnf_secure = $cnf . (exists $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} ? " --host=" . $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} : (exists $ENV{"MYSQL_HOST"} ? " --host=" . $ENV{"MYSQL_HOST"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} ? " --password=" . $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} : (exists $ENV{"MYSQL_PASS"} ? " --password=" . $ENV{"MYSQL_PASS"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_USER"} ? " --user=" . $ENV{"MYSQL_APP_ENV_MYSQL_USER"} : (exists $ENV{"MYSQL_USER"} ? " --user=" . $ENV{"MYSQL_USER"} : q{}));,' -i -e 's,mysql --defaults-file=$cnf,mysql --defaults-file=$cnf_secure,g' /usr/local/bin/denovo_map.pl && \
     sed -i -e 's,$mysql_config;,$mysql_config;\nmy $cnf_secure = $cnf . (exists $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} ? " --host=" . $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} : (exists $ENV{"MYSQL_HOST"} ? " --host=" . $ENV{"MYSQL_HOST"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} ? " --password=" . $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} : (exists $ENV{"MYSQL_PASS"} ? " --password=" . $ENV{"MYSQL_PASS"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_USER"} ? " --user=" . $ENV{"MYSQL_APP_ENV_MYSQL_USER"} : (exists $ENV{"MYSQL_USER"} ? " --user=" . $ENV{"MYSQL_USER"} : q{}));,' -i -e 's,mysql --defaults-file=$cnf,mysql --defaults-file=$cnf_secure,g' /usr/local/bin/ref_map.pl && \
     sed -i -e 's,DBI:mysql:$db:mysql,DBI:mysql:$db:" . (exists $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} ? ";host=" . $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} : (exists $ENV{"MYSQL_HOST"} ? ";host=" . $ENV{"MYSQL_HOST"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} ? ";password=" . $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} : (exists $ENV{"MYSQL_PASS"} ? ";password=" . $ENV{"MYSQL_PASS"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_USER"} ? ";user=" . $ENV{"MYSQL_APP_ENV_MYSQL_USER"} : (exists $ENV{"MYSQL_USER"} ? ";user=" . $ENV{"MYSQL_USER"} : q{})) . ";mysql,g' /usr/local/bin/export_sql.pl && \
-    sed -i -e 's,DBI:mysql:$db:mysql,DBI:mysql:$db:" . (exists $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} ? ";host=" . $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} : (exists $ENV{"MYSQL_HOST"} ? ";host=" . $ENV{"MYSQL_HOST"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} ? ";password=" . $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} : (exists $ENV{"MYSQL_PASS"} ? ";password=" . $ENV{"MYSQL_PASS"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_USER"} ? ";user=" . $ENV{"MYSQL_APP_ENV_MYSQL_USER"} : (exists $ENV{"MYSQL_USER"} ? ";user=" . $ENV{"MYSQL_USER"} : q{})) . ";mysql,g' -i -e 's,$mysql_config;,$mysql_config;\nmy $cnf_secure = $cnf . (exists $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} ? " --host=" . $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} : (exists $ENV{"MYSQL_HOST"} ? " --host=" . $ENV{"MYSQL_HOST"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} ? " --password=" . $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} : (exists $ENV{"MYSQL_PASS"} ? " --password=" . $ENV{"MYSQL_PASS"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_USER"} ? " --user=" . $ENV{"MYSQL_APP_ENV_MYSQL_USER"} : (exists $ENV{"MYSQL_USER"} ? " --user=" . $ENV{"MYSQL_USER"} : q{}));,' -i -e 's,mysql --defaults-file=$cnf,mysql --defaults-file=$cnf_secure,g' /usr/local/bin/index_radabout.tags.pl && \
-    sed -i -e 's,$mysql_config;,$mysql_config;\nmy $cnf_secure = $cnf . (exists $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} ? " --host=" . $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} : (exists $ENV{"MYSQL_HOST"} ? " --host=" . $ENV{"MYSQL_HOST"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} ? " --password=" . $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} : (exists $ENV{"MYSQL_PASS"} ? " --password=" . $ENV{"MYSQL_PASS"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_USER"} ? " --user=" . $ENV{"MYSQL_APP_ENV_MYSQL_USER"} : (exists $ENV{"MYSQL_USER"} ? " --user=" . $ENV{"MYSQL_USER"} : q{}));,' -i -e 's,mysql --defaults-file=$cnf,mysql --defaults-file=$cnf_secure,g' /usr/local/bin/load_radabout.tags.pl && \
+    sed -i -e 's,DBI:mysql:$db:mysql,DBI:mysql:$db:" . (exists $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} ? ";host=" . $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} : (exists $ENV{"MYSQL_HOST"} ? ";host=" . $ENV{"MYSQL_HOST"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} ? ";password=" . $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} : (exists $ENV{"MYSQL_PASS"} ? ";password=" . $ENV{"MYSQL_PASS"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_USER"} ? ";user=" . $ENV{"MYSQL_APP_ENV_MYSQL_USER"} : (exists $ENV{"MYSQL_USER"} ? ";user=" . $ENV{"MYSQL_USER"} : q{})) . ";mysql,g' -i -e 's,$mysql_config;,$mysql_config;\nmy $cnf_secure = $cnf . (exists $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} ? " --host=" . $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} : (exists $ENV{"MYSQL_HOST"} ? " --host=" . $ENV{"MYSQL_HOST"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} ? " --password=" . $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} : (exists $ENV{"MYSQL_PASS"} ? " --password=" . $ENV{"MYSQL_PASS"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_USER"} ? " --user=" . $ENV{"MYSQL_APP_ENV_MYSQL_USER"} : (exists $ENV{"MYSQL_USER"} ? " --user=" . $ENV{"MYSQL_USER"} : q{}));,' -i -e 's,mysql --defaults-file=$cnf,mysql --defaults-file=$cnf_secure,g' /usr/local/bin/index_radtags.pl && \
+    sed -i -e 's,$mysql_config;,$mysql_config;\nmy $cnf_secure = $cnf . (exists $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} ? " --host=" . $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} : (exists $ENV{"MYSQL_HOST"} ? " --host=" . $ENV{"MYSQL_HOST"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} ? " --password=" . $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} : (exists $ENV{"MYSQL_PASS"} ? " --password=" . $ENV{"MYSQL_PASS"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_USER"} ? " --user=" . $ENV{"MYSQL_APP_ENV_MYSQL_USER"} : (exists $ENV{"MYSQL_USER"} ? " --user=" . $ENV{"MYSQL_USER"} : q{}));,' -i -e 's,mysql --defaults-file=$cnf,mysql --defaults-file=$cnf_secure,g' /usr/local/bin/load_radtags.pl && \
     sed -i -e 's,DBI:mysql:$db:mysql,DBI:mysql:$db:" . (exists $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} ? ";host=" . $ENV{"MYSQL_APP_PORT_3306_TCP_ADDR"} : (exists $ENV{"MYSQL_HOST"} ? ";host=" . $ENV{"MYSQL_HOST"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} ? ";password=" . $ENV{"MYSQL_APP_ENV_MYSQL_PASS"} : (exists $ENV{"MYSQL_PASS"} ? ";password=" . $ENV{"MYSQL_PASS"} : q{})) . (exists $ENV{"MYSQL_APP_ENV_MYSQL_USER"} ? ";user=" . $ENV{"MYSQL_APP_ENV_MYSQL_USER"} : (exists $ENV{"MYSQL_USER"} ? ";user=" . $ENV{"MYSQL_USER"} : q{})) . ";mysql,g' /usr/local/bin/load_sequences.pl && \
     cd .. && \
     echo -e "[client]\nport=3306\nlocal-infile=1\n" > /usr/local/share/stacks/sql/mysql.cnf && \