/*
* Author：Henriette-L（3312065512@qq.com）
* Date：2021-3-11
*/
VMware Workstation Pro 14
CentOS 7 64位
FullSSR.pl # https://sourceforge.net/projects/fullssr/.
安装方式
下载后解压
打开终端安装bioperl
[@localhost ~]$ perl -MCPAN -e shell
CPAN.pm requires configuration, but most of it can be done automatically.
If you answer 'no' below, you will enter an interactive dialog for each
configuration option instead.
Would you like to configure as much as possible automatically? [yes]
Autoconfigured everything but 'urllist'.
Now you need to choose your CPAN mirror sites. You can let me
pick mirrors for you, you can select them from a list or you
can enter them by hand.
Would you like me to automatically choose some CPAN mirror
sites for you? (This means connecting to the Internet) [yes]
Trying to fetch a mirror list from the Internet
Fetching with LWP:
http://www.perl.org/CPAN/MIRRORED.BY
Looking for CPAN mirrors near you (please be patient)
...................... done!
New urllist
http://ftp.kr.freebsd.org/pub/CPAN/
http://cpan.uni-altai.ru/
http://mirror.truenetwork.ru/CPAN/
Autoconfiguration complete.
commit: wrote '/home/112shiyanshi/.cpan/CPAN/MyConfig.pm'
You can re-run configuration any time with 'o conf init' in the CPAN shell
Terminal does not support AddHistory.
cpan shell -- CPAN exploration and modules installation (v1.9800)
Enter 'h' for help.
cpan[1]> install Module::Build
./Build install -- OK
cpan[2]> o conf prefer_installer MB
prefer_installer [MB]
Please use 'o conf commit' to make the config permanent!
cpan[3]> o conf commit
commit: wrote '/root/.cpan/CPAN/MyConfig.pm'
cpan[4]> install LWP
Appending installation info to /root/perl5/lib/perl5/x86_64-linux-thread-multi/perllocal.pod
OALDERS/libwww-perl-6.53.tar.gz
/bin/make install -- OK
cpan[5]> install Digest::MD5
Appending installation info to /root/perl5/lib/perl5/x86_64-linux-thread-multi/perllocal.pod
TODDR/Digest-MD5-2.58.tar.gz
/bin/make install -- OK
cpan[6]> d /bioperl/
Distribution BOZO/Fry-Lib-BioPerl-0.15.tar.gz
Distribution CDRAUG/BioPerl-1.7.4.tar.gz
Distribution CDRAUG/Dist-Zilla-PluginBundle-BioPerl-0.27.tar.gz
Distribution CJFIELDS/BioPerl-1.007002.tar.gz
Distribution CJFIELDS/BioPerl-1.6.924.tar.gz
Distribution CJFIELDS/BioPerl-1.7.7.tar.gz
Distribution CJFIELDS/BioPerl-1.7.8.tar.gz
Distribution CJFIELDS/BioPerl-DB-1.006900.tar.gz
Distribution CJFIELDS/BioPerl-Network-1.006902.tar.gz
Distribution CJFIELDS/BioPerl-Run-1.007002.tar.gz
Distribution CJFIELDS/BioPerl-Run-1.007003.tar.gz
Distribution CJFIELDS/Bundle-BioPerl-2.1.9.tar.gz
12 items found
cpan[8]> install CJFIELDS/BioPerl-1.6.924.tar.gz
CJFIELDS/BioPerl-1.6.924.tar.gz
./Build install -- OK
安装插件BioSqIo
cpan[1]> install Module::Build
Reading '/root/.cpan/Metadata'
Database was generated on Sat, 06 Mar 2021 02:55:31 GMT
o confFetching with LWP:
http://www.perl.com/CPAN/authors/01mailrc.txt.gz
oReading '/root/.cpan/sources/authors/01mailrc.txt.gz'
............................................................................DONE
Fetching with LWP:
http://www.perl.com/CPAN/modules/02packages.details.txt.gz
Reading '/root/.cpan/sources/modules/02packages.details.txt.gz'
Database was generated on Mon, 08 Mar 2021 09:41:03 GMT
.............
New CPAN.pm version (v2.28) available.
[Currently running version is v1.9800]
You might want to try
install CPAN
reload cpan
to both upgrade CPAN.pm and run the new version without leaving
the current session.
...............................................................DONE
Fetching with LWP:
http://www.perl.com/CPAN/modules/03modlist.data.gz
Reading '/root/.cpan/sources/modules/03modlist.data.gz'
DONE
Writing /root/.cpan/Metadata
Module::Build is up to date (0.4231).
cpan[2]> o conf prefer_installer MB
Known options:
conf set or get configuration variables
debug set or get debugging options
cpan[3]> o conf commit
commit: wrote '/root/.cpan/CPAN/MyConfig
cpan[4]> install LWP
Appending installation info to /root/perl5/lib/perl5/x86_64-linux-thread-multi/perllocal.pod
OALDERS/libwww-perl-6.53.tar.gz
/bin/make install -- OK
cpan[5]> install Bio::SeqIO
Appending installation info to /root/perl5/lib/perl5/x86_64-linux-thread-multi/perllocal.pod
CJFIELDS/BioPerl-1.7.8.tar.gz
/bin/make install -- OK
cpan[7]> d /bioperl/
Distribution BOZO/Fry-Lib-BioPerl-0.15.tar.gz
Distribution CDRAUG/BioPerl-1.7.4.tar.gz
Distribution CDRAUG/Dist-Zilla-PluginBundle-BioPerl-0.27.tar.gz
Distribution CJFIELDS/BioPerl-1.007002.tar.gz
Distribution CJFIELDS/BioPerl-1.6.924.tar.gz
Distribution CJFIELDS/BioPerl-1.7.7.tar.gz
Distribution CJFIELDS/BioPerl-1.7.8.tar.gz
Distribution CJFIELDS/BioPerl-DB-1.006900.tar.gz
Distribution CJFIELDS/BioPerl-Network-1.006902.tar.gz
Distribution CJFIELDS/BioPerl-Run-1.007002.tar.gz
Distribution CJFIELDS/BioPerl-Run-1.007003.tar.gz
Distribution CJFIELDS/Bundle-BioPerl-2.1.9.tar.gz
12 items found
cpan[9]> install CJFIELDS/BioPerl-1.6.924.tar.gz
CJFIELDS/BioPerl-1.6.924.tar.gz
./Build install -- OK
同理安装FullSSR.pl文件下use的所有BioPerl插件
安装Primer3
[112shiyanshi@localhost ~]$ sudo su
[sudo] 112shiyanshi 的密码：
[root@localhost 112shiyanshi]# sudo apt-get install -y build-essential g++ cmake git-all
sudo: apt-get：找不到命令
[root@localhost 112shiyanshi]# git clone https://github.com/primer3-org/primer3.git primer3
正克隆到 'primer3'...
remote: Enumerating objects: 14, done.
remote: Counting objects: 100% (14/14), done.
remote: Compressing objects: 100% (12/12), done.
remote: Total 7695 (delta 1), reused 7 (delta 1), pack-reused 7681
接收对象中: 100% (7695/7695), 32.35 MiB | 38.00 KiB/s, done.
处理 delta 中: 100% (5668/5668), done.
Checking out files: 100% (689/689), done.
[root@localhost 112shiyanshi]# cd primer3/src
[root@localhost src]# make
no windows
gcc -c -g -Wall -O2 primer3_boulder_main.c
gcc -c -g -Wall -O2 -o format_output.o format_output.c
gcc -c -g -Wall -O2 -o read_boulder.o read_boulder.c
gcc -c -g -Wall -O2 -o print_boulder.o print_boulder.c
g++ -c -g -Wall -O2 -std=c++11 -o libprimer3.o libprimer3.cc
gcc -c -g -Wall -O2 -o p3_seq_lib.o p3_seq_lib.c
ar rv libprimer3.a libprimer3.o p3_seq_lib.o
ar: 正在创建 libprimer3.a
a - libprimer3.o
a - p3_seq_lib.o
ranlib libprimer3.a
gcc -c -g -Wall -O2 -o dpal_primer.o dpal.c
ar rv libdpal.a dpal_primer.o
ar: 正在创建 libdpal.a
a - dpal_primer.o
ranlib libdpal.a
gcc -c -g -Wall -O2 -ffloat-store -o thal_primer.o thal.c
ar rv libthal.a thal_primer.o
ar: 正在创建 libthal.a
a - thal_primer.o
ranlib libthal.a
gcc -c -g -Wall -O2 -ffloat-store -o thal_parameters.o thal_parameters.c
ar rv libthalpara.a thal_parameters.o
ar: 正在创建 libthalpara.a
a - thal_parameters.o
ranlib libthalpara.a
gcc -g -Wall -O2 -c -o oligotm.o oligotm.c
ar rv liboligotm.a oligotm.o
ar: 正在创建 liboligotm.a
a - oligotm.o
ranlib liboligotm.a
gcc -c -g -Wall -O2 masker.c
ar rv libmasker.a masker.o
ar: 正在创建 libmasker.a
a - masker.o
ranlib libmasker.a
g++ -g -Wall -O2 -std=c++11 -lstdc++ -g -o primer3_core primer3_boulder_main.o format_output.o read_boulder.o print_boulder.o libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libmasker.a -lm
gcc -c -g -Wall -o ntdpal_main.o ntdpal_main.c
gcc -c -g -Wall -O2 -o dpal.o dpal.c
gcc -g -o ntdpal ntdpal_main.o dpal.o
gcc -c -g -Wall -O2 -o thal_main.o thal_main.c
gcc -c -g -Wall -O2 -ffloat-store -o thal.o thal.c
gcc -g -o ntthal thal_main.o thal.o thal_parameters.o -lm
gcc -g -Wall -O2 -o oligotm oligotm_main.c liboligotm.a -lm
gcc -g -Wall -O2 -o long_seq_tm_test long_seq_tm_test_main.c oligotm.o -lm
g++ -g -Wall -O2 -std=c++11 -lstdc++ -o primer3_masker masker_main.c libprimer3.a libdpal.a libthal.a libthalpara.a liboligotm.a libmasker.a -lm
[root@localhost src]# make test
no windows
cd ../test; make test
make[1]: 进入目录“/home/112shiyanshi/primer3/test”
cd ../src; make
no windows
make[2]: 进入目录“/home/112shiyanshi/primer3/src”
make[2]: 对“all”无需做任何事。
make[2]: 离开目录“/home/112shiyanshi/primer3/src”
perl cmdline_test.pl
TESTING command line arguments
Test 1... [OK]
Test 2... [OK]
Test 3... [OK]
Test 4... [OK]
Test 5... [OK]
Passed all tests - [OK]
perl oligotm_test.pl
TESTING Tm CALCULATIONS
Tm tests nr 1-50: [OK]
echo; echo; echo 'TESTING ALIGNMENT CALCS'; echo; perl dpal_test.pl ;
TESTING ALIGNMENT CALCS
Error handling of too-long sequence...[OK]
Default implementations + alignment...[OK]
Default implementations + NO alignment 1...[OK]
Default implementations + NO alignment 2...[OK]
Force _dpal_generic...[OK]
Force _dpal_long_nopath_generic 1...[OK]
Force _dpal_long_nopath_generic 2...[OK]
Force long maxgap1 functions 1...[OK]
Force long maxgap1 functions 2...[OK]
echo; echo; echo 'TESTING THERMODYNAMIC ALIGNMENT CALCS'; echo; perl thal_test.pl ;
TESTING THERMODYNAMIC ALIGNMENT CALCS
Error handling of too-long sequence...
1................................... [OK]
Default implementations + alignment...[OK]
Default implementations + NO alignment 1...[OK]
Default implementations + NO alignment 2...[OK]
echo; echo; echo 'TESTING MASKER'; echo; perl masker_test.pl ;
TESTING MASKER
Default implementations...[OK]
echo; echo; echo 'TESTING primer3_core'; echo; perl p3test.pl
TESTING primer3_core
mkdir: ../test/primer_list_tmp
mkdir: ../test/primer1_list_tmp
mkdir: ../test/primer1_th_list_tmp
mkdir: ../test/th-w-other-tasks_list_tmp
p3test.pl for primer3_core version 2.5.0
p3test.pl: testing ../src/primer3_core
START, Tue Mar 9 12:51:02 2021
testing fatal errors...
./primer_global_err/bad_divalent_dntp_conc_1
Testing --output and --error flags on
../src/primer3_core --strict_tags ./primer_global_err/bad_divalent_dntp_conc_1.in --output ./primer_global_err/bad_divalent_dntp_conc_1.tmp --error ./primer_global_err/bad_divalent_dntp_conc_1.tmp2
./primer_global_err/bad_divalent_dntp_conc_2
./primer_global_err/bad_divalent_dntp_conc_3
./primer_global_err/bad_divalent_dntp_conc_4
./primer_global_err/bad_dna_conc
./primer_global_err/bad_first_base_index
./primer_global_err/bad_float_1
./primer_global_err/bad_float_2
./primer_global_err/bad_float_3
./primer_global_err/bad_float_4
./primer_global_err/bad_gc_1
./primer_global_err/bad_gc_2
./primer_global_err/bad_gc_3
./primer_global_err/bad_gc_int_1
./primer_global_err/bad_gc_int_2
./primer_global_err/bad_gc_int_3
./primer_global_err/bad_min_three_prime_distance
./primer_global_err/bad_num_ns
./primer_global_err/bad_num_ns_int
./primer_global_err/bad_product_sizes_1
./primer_global_err/bad_product_sizes_2
./primer_global_err/bad_product_sizes_3
./primer_global_err/bad_product_sizes_4
./primer_global_err/bad_salt_conc
./primer_global_err/bad_self_any
./primer_global_err/bad_self_any_int
./primer_global_err/bad_self_end
./primer_global_err/bad_self_end_int
./primer_global_err/bad_settings0
./primer_global_err/bad_settings1
./primer_global_err/bad_settings2
./primer_global_err/bad_settings3
./primer_global_err/bad_settings4
./primer_global_err/bad_settings5
./primer_global_err/bad_settings6
./primer_global_err/empty_1
./primer_global_err/empty_product_size
./primer_global_err/gc_clamp_min_size
./primer_global_err/incorrect_task
./primer_global_err/io_gc_content_obj_fn
./primer_global_err/io_obj_fn
./primer_global_err/junction_overlap_max_size
./primer_global_err/junction_overlap_min_size
./primer_global_err/max_min_tm
./primer_global_err/max_min_tm_int
./primer_global_err/max_opt_tm
./primer_global_err/max_opt_tm_int
./primer_global_err/MAX_PRIMER_LENGTH
./primer_global_err/max_size_limit_int
./primer_global_err/max_size_min_product
./primer_global_err/max_size_min_product_int
./primer_global_err/min_opt_tm
./primer_global_err/min_opt_tm_int
./primer_global_err/mishyb_obj_fn
./primer_global_err/mispr_obj_fn
./primer_global_err/must_match_length_0
./primer_global_err/must_match_length_1
./primer_global_err/must_match_length_10
./primer_global_err/must_match_length_2
./primer_global_err/must_match_length_3
./primer_global_err/must_match_length_4
./primer_global_err/must_match_length_5
./primer_global_err/must_match_length_6
./primer_global_err/must_match_length_7
./primer_global_err/must_match_length_8
./primer_global_err/must_match_length_9
./primer_global_err/no_equal
./primer_global_err/no_terminal_equal
./primer_global_err/opt_max_size
./primer_global_err/opt_max_size_int
./primer_global_err/opt_min_size
./primer_global_err/opt_min_size_int
./primer_global_err/pair_mispr
./primer_global_err/pr_gc_content_obj_fn
./primer_global_err/product_size_obj_fn
./primer_global_err/product_tm_obj_fn
./primer_global_err/repeat_lib_err
./primer_global_err/repeat_lib_err1
./primer_global_err/repeat_lib_err2
./primer_global_err/repeat_lib_err3
./primer_global_err/repeat_lib_err4
./primer_global_err/repeat_lib_err5
./primer_global_err/repeat_lib_err6
./primer_global_err/repeat_lib_int_err
./primer_global_err/repeat_lib_int_err1
./primer_global_err/repeat_lib_int_err2
./primer_global_err/repeat_lib_int_err3
./primer_global_err/repeat_lib_int_err4
./primer_global_err/repeat_lib_int_err5
./primer_global_err/repeat_lib_int_err6
./primer_global_err/seq_quality1
./primer_global_err/seq_quality2
./primer_global_err/seq_quality3
./primer_global_err/seq_quality4
./primer_global_err/too_many_product_sizes
./primer_global_err/zero_min_size
./primer_global_err/zero_num_return
[OK]
primer_must_use_th...0s [OK]
primer_sec_struct_dpal...0s [OK]
primer_task_th...2s [OK]
primer_thal_args...1s [OK]
primer_thal_max_seq_error...1s [OK]
primer_first_base_index...0s [OK]
primer_must_match...0s [OK]
primer_masker...7s [OK]
primer_masker_formatted...6s [OK]
test_compl_error...0s [OK]
test_left_to_right_of_right...0s [OK]
dv_conc_vs_dntp_conc...0s [OK]
primer_boundary...1s [OK]
primer_boundary1...0s [OK]
primer_boundary_formatted...0s [OK]
primer_boundary1_formatted...0s [OK]
primer3_v1_1_4_default_settings...0s [OK]
primer3web_v0_4_0_default_settings...0s [OK]
primer3web_v3_0_0_default_settings...2s [OK]
primer3web_v4_0_0_default_settings...1s [OK]
primer_internal...0s [OK]
primer_internal1...0s [OK]
primer_internal_formatted...0s [OK]
primer_internal1_formatted...0s [OK]
primer_ok_regions...0s [OK]
primer_ok_regions_formatted...0s [OK]
primer_ok_regions2...8s [OK]
primer_tm_lc_masking...0s [OK]
primer_tm_lc_masking_formatted...0s [OK]
primer_start_codon...1s [OK]
primer_task...0s [OK]
primer_task_formatted...0s [OK]
primer_renewed_tasks...0s [OK]
primer_new_tasks...0s [OK]
primer_new_tasks_formatted...1s [OK]
primer_windows_newlines...1s [OK]
primer_must_overlap_point...1s [OK]
primer_overlap_junction...0s [OK]
primer_all_settingsfiles...0s [OK]
primer_high_tm_load_set...0s [OK]
primer_high_gc_load_set...0s [OK]
primer_gc_end...0s [OK]
primer_check...0s [OK]
primer_must_use...0s [OK]
primer_must_use_formatted...0s [OK]
primer_syntax...0s [OK]
primer_end_pathology...0s [OK]
primer_num_best...0s [OK]
primer_quality_boundary...1s [OK]
primer...1s [OK]
primer_list_files...[OK]
primer1...0s [OK]
primer1_list_files...[OK]
primer_mispriming...1s [OK]
primer_mispriming_formatted...0s [OK]
primer_mispriming_boundary1...0s [OK]
primer_mispriming_boundary1_formatted...0s [OK]
primer_mispriming_boundary2...0s [OK]
primer_mispriming_boundary2_formatted...0s [OK]
primer_mispriming_long_lib...1s [OK]
primer_rat...0s [OK]
primer_human...2s [OK]
long_seq...0s [OK]
primer_position_penalty...1s [OK]
primer_position_penalty_formatted...0s [OK]
p3-tmpl-mispriming...1s [OK]
primer_three_prime_distance...0s [OK]
primer_obj_fn...3s [OK]
p3_3_prime_n...1s [OK]
primer_masker...4s [OK]
primer_masker_formatted...3s [OK]
primer_mispriming_th...10s [OK]
th-w-other-tasks...16s [OK]
th-w-other-tasks_list_files...[OK]
primer_new_tasks_th...21s [OK]
primer_sec_struct_thal...22s [OK]
primer_thermod_align...63s [OK]
primer_thermod_align_formatted...46s [OK]
primer1_th...141s [OK]
primer1_th_list_files...[OK]
primer_lib_amb_codes...
NOTE: this test takes _much_ longer than the others (5 to 20 minutes or more).
starting primer_lib_amb_codes at Tue Mar 9 12:57:20 2021...165s [OK]
Tests in p3test.pl ran for 543 s (9.05 min)
DONE Tue Mar 9 13:00:05 2021 Passed all tests - [OK]
echo; echo; echo "Testing completed. You must check the test output for the string FAILED"; echo; echo;
Testing completed. You must check the test output for the string FAILED
make[1]: 离开目录“/home/112shiyanshi/primer3/test”
以上插件安装完毕
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