[Bioperl-l] Installing Bioperl on Mac OS X 10.5.7

stephenmcgowan1 stevey_mac2k2 at hotmail.com
Sun Jun 28 06:53:04 EDT 2009


Hi,

I'm new to the mac way of working and programming aswell as the UNIX
(Terminal) environment. I will describe in as much detail as i can as to
what i have done so far in terms of bioperl installation and try to describe
what my problem is.

Ok so first of all i have downloaded and extracted the files BioPerl-1.6.0
and BioPerl-db-1.6.0 from the site. I have these two folders saved in a
folder on my OSX desktop called "ExerciseTwo".

After doing this, i open up Terminal and locate BioPerl-1.6.0.

i then run:

perl Build.PL (i have also tried sudo perl Build.pl)

i then run ./Build test (again tried this with sudo ./Build test)

after running the build test, i receive the feedback:

Failed Test                              Stat Wstat Total Fail  Failed  List
of Failed
-------------------------------------------------------------------------------
t/AlignIO/AlignIO.t                    255 65280    28   42 150.00%  8-28
t/AlignIO/arp.t                         255 65280    48   92 191.67%  3-48
t/Annotation/Annotation.t          255 65280   159   83  52.20%  9 117
119-159
t/ClusterIO/SequenceFamily.t    255 65280    19   34 178.95%  3-19
t/LocalDB/Flat.t                       255 65280    24   20  83.33%  15-24
t/LocalDB/Index.t                     255 65280    64   66 103.12%  32-64
t/RemoteDB/BioFetch.t              255 65280    36    2   5.56%  36
t/RemoteDB/DB.t                      3   768   113   59  52.21%  83-113
t/RemoteDB/EUtilities.t              1   256   309    1   0.32%  307
t/SeqIO/Handler.t                     255 65280   550 1098 199.64%  2-550
t/SeqIO/chaos.t                        1   256     8    1  12.50%  1
t/SeqIO/swiss.t                        255 65280   240  479 199.58%  1-240
t/SeqTools/GuessSeqFormat.t          1   256    49    2   4.08%  25 50
t/Tools/Analysis/Protein/ELM.t     255 65280    15   22 146.67%  5-15
t/Tools/Analysis/Protein/Scansite  255 65280    14   20 142.86%  5-14
t/Tools/Run/WrapperBase.t            1   256    27    1   3.70%  20
44 tests and 250 subtests skipped.
Failed 16/318 test scripts, 94.97% okay. 1015/15518 subtests failed, 93.46%
okay

Ok so going off this i then decide to run the install: ./Build install

This is a segment of the info i receive back in Terminal after the install:

Manifying blib/script/bp_pairwise_kaks.pl ->
blib/bindoc/bp_pairwise_kaks.pl.1
Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1
Manifying blib/script/bp_seq_length.pl -> blib/bindoc/bp_seq_length.pl.1
Manifying blib/script/bp_query_entrez_taxa.pl ->
blib/bindoc/bp_query_entrez_taxa.pl.1
Manifying blib/script/bp_load_gff.pl -> blib/bindoc/bp_load_gff.pl.1
Manifying blib/script/bp_fastam9_to_table.pl ->
blib/bindoc/bp_fastam9_to_table.pl.1
Manifying blib/script/bp_process_wormbase.pl ->
blib/bindoc/bp_process_wormbase.pl.1
Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1
Manifying blib/script/bp_composite_LD.pl -> blib/bindoc/bp_composite_LD.pl.1
Manifying blib/script/bp_classify_hits_kingdom.pl ->
blib/bindoc/bp_classify_hits_kingdom.pl.1
Manifying blib/script/bp_blast2tree.pl -> blib/bindoc/bp_blast2tree.pl.1
Manifying blib/script/bp_heterogeneity_test.pl ->
blib/bindoc/bp_heterogeneity_test.pl.1
Manifying blib/script/bp_generate_histogram.pl ->
blib/bindoc/bp_generate_histogram.pl.1
Manifying blib/script/bp_process_gadfly.pl ->
blib/bindoc/bp_process_gadfly.pl.1
mkdir /usr/local/share: Permission denied at
/System/Library/Perl/5.8.8/ExtUtils/Install.pm line 112

now these bp_files such as bp_nrdb.pl should be installed onto my Unix
somewhere? but i'm not sure if the install has worked, and these files saved
to the made directory, as is the case here:

mkdir /usr/local/share: Permission denied at
/System/Library/Perl/5.8.8/ExtUtils/Install.pm line 112

is there something wrong with my install? i think /usr/local/share should be
created and then all of these bp_files should go into this folder. Is there
anything that i'm doing wrong here?

Thanks

Stephen.



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