StephenMcGowan
asked on
Bioperl installation issue.
Hi,
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/E LM.t 255 65280 15 22 146.67% 5-15
t/Tools/Analysis/Protein/S cansite 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_ka ks.pl -> blib/bindoc/bp_pairwise_ka ks.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_entre z_taxa.pl -> blib/bindoc/bp_query_entre z_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_wor mbase.pl -> blib/bindoc/bp_process_wor mbase.pl.1
Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1
Manifying blib/script/bp_composite_L D.pl -> blib/bindoc/bp_composite_L D.pl.1
Manifying blib/script/bp_classify_hi ts_kingdom .pl -> blib/bindoc/bp_classify_hi ts_kingdom .pl.1
Manifying blib/script/bp_blast2tree. pl -> blib/bindoc/bp_blast2tree. pl.1
Manifying blib/script/bp_heterogenei ty_test.pl -> blib/bindoc/bp_heterogenei ty_test.pl .1
Manifying blib/script/bp_generate_hi stogram.pl -> blib/bindoc/bp_generate_hi stogram.pl .1
Manifying blib/script/bp_process_gad fly.pl -> blib/bindoc/bp_process_gad fly.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.
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/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/Tools/Analysis/Protein/E
t/Tools/Analysis/Protein/S
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_ka
Manifying blib/script/bp_seqret.pl -> blib/bindoc/bp_seqret.pl.1
Manifying blib/script/bp_seq_length.
Manifying blib/script/bp_query_entre
Manifying blib/script/bp_load_gff.pl
Manifying blib/script/bp_fastam9_to_
Manifying blib/script/bp_process_wor
Manifying blib/script/bp_nrdb.pl -> blib/bindoc/bp_nrdb.pl.1
Manifying blib/script/bp_composite_L
Manifying blib/script/bp_classify_hi
Manifying blib/script/bp_blast2tree.
Manifying blib/script/bp_heterogenei
Manifying blib/script/bp_generate_hi
Manifying blib/script/bp_process_gad
mkdir /usr/local/share: Permission denied at /System/Library/Perl/5.8.8
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
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.
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.
ASKER
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?
Thanks.
Stephen.
thanks for the feedback. How would i change the permissions in the System/Library/Perl/5.8.8/
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?
Thanks.
Stephen.
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.
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.
ASKER
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?
Thanks,
Stephen.
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?
Thanks,
Stephen.
ASKER CERTIFIED SOLUTION
membership
This solution is only available to members.
To access this solution, you must be a member of Experts Exchange.
ASKER
righty,
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.
Stephen.
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/
Can you simply change the permissions of the directory by trying "chmod System/Library/Perl/5.8.8/
i'll have a look into this now that i'm in this super level.
Thanks tera.
Stephen.
Once you have su access, you can probably have permsision to write to all the install directories and may not need to use chmod
ASKER
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.
I will give this a shot.
Yes, hopefully it should just work with su access.