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Bioperl installation issue.

Medium Priority
Last Modified: 2012-05-07

This is a relatively specialised question regarding the Bioperl package, so i'm not sure if anybody uses this and has any insight on the installation of this perl programme, i'm kinda throwing this question on here as a last resort.

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?

Watch Question

Kim RyanIT Consultant

You will need to check  the permisions in the t /System/Library/Perl/5.8.8/ area. You may need to login as super user to do the install. Apart from that, all looks OK.


Hi teraplane,

thanks for the feedback. How would i change the permissions in the System/Library/Perl/5.8.8/ area to get around this?

also how would i login as super user to do the install? I'm kinda brand new to any of this... would you be able to guide me through this problem?


Kim RyanIT Consultant

On unix and mac systems, ther is alway a super user account, but you will need to know the password.

To login type
su password

You can change directory permisions with the chmod command, but again will probably need the super user password to do this.


hmm i type "su" and yeah, it asks for a password.

I type in, what i'm guessing is my password (not really 100% sure on it) and receive:

su: Sorry

I'm guessing my password is wrong, is there anyway i can retrieve the password?


IT Consultant
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just got into supervisor level i think. My command line reads:     bash-3.2#

i'll have a look at using chmod to change the permissions of the System/Library/Perl/5.8.8/ area.

Can you simply change the permissions of the directory by trying "chmod System/Library/Perl/5.8.8/ 755"?

i'll have a look into this now that i'm in this super level.

Thanks tera.

Kim RyanIT Consultant

Once you have su access, you can probably have permsision to write to all the install directories and may not need to use chmod


are you saying once i have su access i can just run the installs, and they should just go through without any hitches or errors?

I will give this a shot.
Kim RyanIT Consultant

Yes, hopefully it should just work with su access.
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