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mahmoodn

perl Build.PL

mahmoodn
Jun 25th, 2017
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  1. [mahmood@cluster ~]$ cd
  2. [mahmood@cluster ~]$ mkdir src
  3. [mahmood@cluster ~]$ cd src
  4. [mahmood@cluster src]$ wget ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz
  5. --2017-06-25 23:42:36-- ftp://ftp.ensembl.org/pub/ensembl-api.tar.gz
  6. => "ensembl-api.tar.gz"
  7. Resolving ftp.ensembl.org... 193.62.193.8
  8. Connecting to ftp.ensembl.org|193.62.193.8|:21... connected.
  9. Logging in as anonymous ... Logged in!
  10. ==> SYST ... done. ==> PWD ... done.
  11. ==> TYPE I ... done. ==> CWD (1) /pub ... done.
  12. ==> SIZE ensembl-api.tar.gz ... 59733883
  13. ==> PASV ... done. ==> RETR ensembl-api.tar.gz ... done.
  14. Length: 59733883 (57M) (unauthoritative)
  15.  
  16. 100%[===================================================================================>] 59,733,883 111K/s in 22m 25s
  17.  
  18. 2017-06-26 00:05:05 (43.4 KB/s) - "ensembl-api.tar.gz" saved [59733883]
  19.  
  20. [mahmood@cluster src]$ wget https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
  21. --2017-06-26 00:05:13-- https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
  22. Resolving cpan.metacpan.org... 151.101.128.249, 151.101.192.249, 151.101.0.249, ...
  23. Connecting to cpan.metacpan.org|151.101.128.249|:443... connected.
  24. ERROR: certificate common name "a.ssl.fastly.net" doesn't match requested host name "cpan.metacpan.org".
  25. To connect to cpan.metacpan.org insecurely, use '--no-check-certificate'.
  26. [mahmood@cluster src]$ wget https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz --no-check-certificate
  27. --2017-06-26 00:05:28-- https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.1.tar.gz
  28. Resolving cpan.metacpan.org... 151.101.192.249, 151.101.0.249, 151.101.64.249, ...
  29. Connecting to cpan.metacpan.org|151.101.192.249|:443... connected.
  30. WARNING: certificate common name "a.ssl.fastly.net" doesn't match requested host name "cpan.metacpan.org".
  31. HTTP request sent, awaiting response... 200 OK
  32. Length: 10462526 (10.0M) [application/x-gzip]
  33. Saving to: "BioPerl-1.6.1.tar.gz"
  34.  
  35. 100%[===================================================================================>] 10,462,526 117K/s in 90s
  36.  
  37. 2017-06-26 00:07:01 (114 KB/s) - "BioPerl-1.6.1.tar.gz" saved [10462526/10462526]
  38.  
  39. [mahmood@cluster src]$ tar zxf ensembl-api.tar.gz
  40. [mahmood@cluster src]$ tar zxf BioPerl-1.6.1.tar.gz
  41. [mahmood@cluster src]$ vim ../.bashrc
  42. [mahmood@cluster src]$ cat ../.bashrc
  43. # .bashrc
  44. # Source global definitions
  45. if [ -f /etc/bashrc ]; then
  46. . /etc/bashrc
  47. fi
  48. # User specific aliases and functions
  49. PERL5LIB=${PERL5LIB}:${HOME}/src/bioperl-1.6.1
  50. PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl/modules
  51. PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-compara/modules
  52. PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-variation/modules
  53. PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-funcgen/modules
  54. export PERL5LIB
  55. [mahmood@cluster src]$ source ../.bashrc
  56. [mahmood@cluster src]$ cd ~/src
  57. [mahmood@cluster src]$ git clone --branch master --depth 1 https://github.com/samtools/htslib.git
  58. Cloning into 'htslib'...
  59. remote: Counting objects: 211, done.
  60. remote: Compressing objects: 100% (181/181), done.
  61. remote: Total 211 (delta 29), reused 90 (delta 18), pack-reused 0
  62. Receiving objects: 100% (211/211), 1.19 MiB | 93 KiB/s, done.
  63. Resolving deltas: 100% (29/29), done.
  64. [mahmood@cluster src]$ cd htslib
  65. [mahmood@cluster htslib]$ make
  66. gcc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c
  67. gcc -g -Wall -O2 -I. -c -o knetfile.o knetfile.c
  68. gcc -g -Wall -O2 -I. -c -o kstring.o kstring.c
  69. gcc -g -Wall -O2 -I. -c -o bcf_sr_sort.o bcf_sr_sort.c
  70. gcc -g -Wall -O2 -I. -c -o bgzf.o bgzf.c
  71. gcc -g -Wall -O2 -I. -c -o errmod.o errmod.c
  72. gcc -g -Wall -O2 -I. -c -o faidx.o faidx.c
  73. gcc -g -Wall -O2 -I. -c -o hfile.o hfile.c
  74. gcc -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c
  75. echo '#define HTS_VERSION "1.5"' > version.h
  76. gcc -g -Wall -O2 -I. -c -o hts.o hts.c
  77. gcc -g -Wall -O2 -I. -c -o md5.o md5.c
  78. gcc -g -Wall -O2 -I. -c -o multipart.o multipart.c
  79. gcc -g -Wall -O2 -I. -c -o probaln.o probaln.c
  80. gcc -g -Wall -O2 -I. -c -o realn.o realn.c
  81. gcc -g -Wall -O2 -I. -c -o regidx.o regidx.c
  82. gcc -g -Wall -O2 -I. -c -o sam.o sam.c
  83. gcc -g -Wall -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c
  84. gcc -g -Wall -O2 -I. -c -o vcf_sweep.o vcf_sweep.c
  85. gcc -g -Wall -O2 -I. -c -o tbx.o tbx.c
  86. gcc -g -Wall -O2 -I. -c -o textutils.o textutils.c
  87. gcc -g -Wall -O2 -I. -c -o thread_pool.o thread_pool.c
  88. gcc -g -Wall -O2 -I. -c -o vcf.o vcf.c
  89. gcc -g -Wall -O2 -I. -c -o vcfutils.o vcfutils.c
  90. gcc -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c
  91. gcc -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c
  92. gcc -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c
  93. gcc -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c
  94. gcc -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c
  95. gcc -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c
  96. gcc -g -Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c
  97. gcc -g -Wall -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c
  98. gcc -g -Wall -O2 -I. -c -o cram/files.o cram/files.c
  99. gcc -g -Wall -O2 -I. -c -o cram/mFILE.o cram/mFILE.c
  100. gcc -g -Wall -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c
  101. gcc -g -Wall -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c
  102. gcc -g -Wall -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c
  103. gcc -g -Wall -O2 -I. -c -o cram/sam_header.o cram/sam_header.c
  104. gcc -g -Wall -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c
  105. ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o
  106. ranlib libhts.a
  107. gcc -g -Wall -O2 -I. -fpic -c -o kfunc.pico kfunc.c
  108. gcc -g -Wall -O2 -I. -fpic -c -o knetfile.pico knetfile.c
  109. gcc -g -Wall -O2 -I. -fpic -c -o kstring.pico kstring.c
  110. gcc -g -Wall -O2 -I. -fpic -c -o bcf_sr_sort.pico bcf_sr_sort.c
  111. gcc -g -Wall -O2 -I. -fpic -c -o bgzf.pico bgzf.c
  112. gcc -g -Wall -O2 -I. -fpic -c -o errmod.pico errmod.c
  113. gcc -g -Wall -O2 -I. -fpic -c -o faidx.pico faidx.c
  114. gcc -g -Wall -O2 -I. -fpic -c -o hfile.pico hfile.c
  115. gcc -g -Wall -O2 -I. -fpic -c -o hfile_net.pico hfile_net.c
  116. gcc -g -Wall -O2 -I. -fpic -c -o hts.pico hts.c
  117. gcc -g -Wall -O2 -I. -fpic -c -o md5.pico md5.c
  118. gcc -g -Wall -O2 -I. -fpic -c -o multipart.pico multipart.c
  119. gcc -g -Wall -O2 -I. -fpic -c -o probaln.pico probaln.c
  120. gcc -g -Wall -O2 -I. -fpic -c -o realn.pico realn.c
  121. gcc -g -Wall -O2 -I. -fpic -c -o regidx.pico regidx.c
  122. gcc -g -Wall -O2 -I. -fpic -c -o sam.pico sam.c
  123. gcc -g -Wall -O2 -I. -fpic -c -o synced_bcf_reader.pico synced_bcf_reader.c
  124. gcc -g -Wall -O2 -I. -fpic -c -o vcf_sweep.pico vcf_sweep.c
  125. gcc -g -Wall -O2 -I. -fpic -c -o tbx.pico tbx.c
  126. gcc -g -Wall -O2 -I. -fpic -c -o textutils.pico textutils.c
  127. gcc -g -Wall -O2 -I. -fpic -c -o thread_pool.pico thread_pool.c
  128. gcc -g -Wall -O2 -I. -fpic -c -o vcf.pico vcf.c
  129. gcc -g -Wall -O2 -I. -fpic -c -o vcfutils.pico vcfutils.c
  130. gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_codecs.pico cram/cram_codecs.c
  131. gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_decode.pico cram/cram_decode.c
  132. gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_encode.pico cram/cram_encode.c
  133. gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_external.pico cram/cram_external.c
  134. gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_index.pico cram/cram_index.c
  135. gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_io.pico cram/cram_io.c
  136. gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_samtools.pico cram/cram_samtools.c
  137. gcc -g -Wall -O2 -I. -fpic -c -o cram/cram_stats.pico cram/cram_stats.c
  138. gcc -g -Wall -O2 -I. -fpic -c -o cram/files.pico cram/files.c
  139. gcc -g -Wall -O2 -I. -fpic -c -o cram/mFILE.pico cram/mFILE.c
  140. gcc -g -Wall -O2 -I. -fpic -c -o cram/open_trace_file.pico cram/open_trace_file.c
  141. gcc -g -Wall -O2 -I. -fpic -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
  142. gcc -g -Wall -O2 -I. -fpic -c -o cram/rANS_static.pico cram/rANS_static.c
  143. gcc -g -Wall -O2 -I. -fpic -c -o cram/sam_header.pico cram/sam_header.c
  144. gcc -g -Wall -O2 -I. -fpic -c -o cram/string_alloc.pico cram/string_alloc.c
  145. gcc -shared -Wl,-soname,libhts.so.2 -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico -lz -lm -lbz2 -llzma -lpthread
  146. ln -sf libhts.so libhts.so.2
  147. gcc -g -Wall -O2 -I. -c -o bgzip.o bgzip.c
  148. gcc -o bgzip bgzip.o libhts.a -lz -lm -lbz2 -llzma -lpthread
  149. gcc -g -Wall -O2 -I. -c -o htsfile.o htsfile.c
  150. gcc -o htsfile htsfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread
  151. gcc -g -Wall -O2 -I. -c -o tabix.o tabix.c
  152. gcc -o tabix tabix.o libhts.a -lz -lm -lbz2 -llzma -lpthread
  153. gcc -g -Wall -O2 -I. -c -o test/hts_endian.o test/hts_endian.c
  154. test/hts_endian.c: In function 't_double':
  155. ./htslib/hts_endian.h:152: warning: dereferencing pointer 'buf.17' does break strict-aliasing rules
  156. ./htslib/hts_endian.h:152: note: initialized from here
  157. ./htslib/hts_endian.h:152: warning: dereferencing pointer 'buf.17' does break strict-aliasing rules
  158. ./htslib/hts_endian.h:152: note: initialized from here
  159. test/hts_endian.c: In function 't_float':
  160. ./htslib/hts_endian.h:136: warning: dereferencing pointer 'buf.16' does break strict-aliasing rules
  161. ./htslib/hts_endian.h:136: note: initialized from here
  162. ./htslib/hts_endian.h:136: warning: dereferencing pointer 'buf.16' does break strict-aliasing rules
  163. ./htslib/hts_endian.h:136: note: initialized from here
  164. gcc -o test/hts_endian test/hts_endian.o -lz -lm -lbz2 -llzma
  165. gcc -g -Wall -O2 -I. -c -o test/fieldarith.o test/fieldarith.c
  166. gcc -o test/fieldarith test/fieldarith.o libhts.a -lz -lm -lbz2 -llzma -lpthread
  167. gcc -g -Wall -O2 -I. -c -o test/hfile.o test/hfile.c
  168. gcc -o test/hfile test/hfile.o libhts.a -lz -lm -lbz2 -llzma -lpthread
  169. gcc -g -Wall -O2 -I. -c -o test/sam.o test/sam.c
  170. gcc -o test/sam test/sam.o libhts.a -lz -lm -lbz2 -llzma -lpthread
  171. gcc -g -Wall -O2 -I. -c -o test/test_bgzf.o test/test_bgzf.c
  172. gcc -o test/test_bgzf test/test_bgzf.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread
  173. gcc -g -Wall -O2 -I. -c -o test/test-regidx.o test/test-regidx.c
  174. gcc -o test/test-regidx test/test-regidx.o libhts.a -lz -lm -lbz2 -llzma -lpthread
  175. gcc -g -Wall -O2 -I. -c -o test/test_view.o test/test_view.c
  176. gcc -o test/test_view test/test_view.o libhts.a -lz -lm -lbz2 -llzma -lpthread
  177. gcc -g -Wall -O2 -I. -c -o test/test-vcf-api.o test/test-vcf-api.c
  178. gcc -o test/test-vcf-api test/test-vcf-api.o libhts.a -lz -lm -lbz2 -llzma -lpthread
  179. gcc -g -Wall -O2 -I. -c -o test/test-vcf-sweep.o test/test-vcf-sweep.c
  180. gcc -o test/test-vcf-sweep test/test-vcf-sweep.o libhts.a -lz -lm -lbz2 -llzma -lpthread
  181. gcc -g -Wall -O2 -I. -c -o test/test-bcf-sr.o test/test-bcf-sr.c
  182. gcc -o test/test-bcf-sr test/test-bcf-sr.o libhts.a -lz -lz -lm -lbz2 -llzma -lpthread
  183. [mahmood@cluster htslib]$ export HTSLIB_DIR=${HOME}/src/htslib/
  184. [mahmood@cluster htslib]$ cd ..
  185. [mahmood@cluster src]$ git clone https://github.com/Ensembl/Bio-DB-HTS.git
  186. Cloning into 'Bio-DB-HTS'...
  187. remote: Counting objects: 2972, done.
  188. remote: Compressing objects: 100% (13/13), done.
  189. remote: Total 2972 (delta 4), reused 12 (delta 3), pack-reused 2954
  190. Receiving objects: 100% (2972/2972), 9.84 MiB | 110 KiB/s, done.
  191. Resolving deltas: 100% (1587/1587), done.
  192. [mahmood@cluster src]$ cd Bio-DB-HTS
  193. [mahmood@cluster Bio-DB-HTS]$ perl Build.PL
  194. Can't locate Module/Build.pm in @INC (@INC contains: /export/home/mahmood/src/bioperl-1.6.1 /export/home/mahmood/src/ensembl/modules /export/home/mahmood/src/ensembl-compara/modules /export/home/mahmood/src/ensembl-variation/modules /export/home/mahmood/src/ensembl-funcgen/modules /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at Build.PL line 20.
  195. BEGIN failed--compilation aborted at Build.PL line 20.
  196. [mahmood@cluster Bio-DB-HTS]$
  197.  
  198.  
  199. --
  200. Regards,
  201. Mahmood
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