[Biopython] Permissions for Bio, BioSQL, Martel

[Finsen Chiu]

Hi all,

What should the correct permission settings be for the Bio, BioSQL, 
Martel directories and its sub folders/files?

When I install biopython as root, the directories and files created have 
permissions of either 600 or 400, which is not very helpful if I am 
installing as a sys admin since other users can't import anything.

I also tried doing a umask 022 before installing and encountered write 
permission for non-root users, as followed:

======================================================================
ERROR: test_Clustalw_tool
----------------------------------------------------------------------
[Errno 13] Permission denied: 'Clustalw/temp horses.fasta'
======================================================================
ERROR: Ensure that we can write proper FASTA output files.
----------------------------------------------------------------------
Traceback (most recent call last):
 File "test_Motif.py", line 65, in test_FAoutput
   output_handle = open(self.FAout, "w")
IOError: [Errno 13] Permission denied: 'Motif/fa.out'

======================================================================
ERROR: Ensure that we can write proper TransFac output files.
----------------------------------------------------------------------
Traceback (most recent call last):
 File "test_Motif.py", line 72, in test_TFoutput
   output_handle = open(self.TFout, "w")
IOError: [Errno 13] Permission denied: 'Motif/tf.out'

======================================================================
ERROR: Ensure that we can write proper pfm output files.
----------------------------------------------------------------------
Traceback (most recent call last):
 File "test_Motif.py", line 79, in test_pfm_output
   output_handle = open(self.PFMout, "w")
IOError: [Errno 13] Permission denied: 'Motif/fa.out'

======================================================================
ERROR: Reading and writing motifs to a file
----------------------------------------------------------------------
Traceback (most recent call last):
 File "test_NNGene.py", line 48, in test_motif
   output_handle = open(self.test_file, "w")
IOError: [Errno 13] Permission denied: 'NeuralNetwork/patternio.txt'

======================================================================
ERROR: Reading and writing schemas to a file.
----------------------------------------------------------------------
Traceback (most recent call last):
 File "test_NNGene.py", line 81, in test_schema
   output_handle = open(self.test_file, "w")
IOError: [Errno 13] Permission denied: 'NeuralNetwork/patternio.txt'

======================================================================
ERROR: Reading and writing signatures to a file.
----------------------------------------------------------------------
Traceback (most recent call last):
 File "test_NNGene.py", line 114, in test_signature
   output_handle = open(self.test_file, "w")
IOError: [Errno 13] Permission denied: 'NeuralNetwork/patternio.txt'

======================================================================
ERROR: Full template creation test
----------------------------------------------------------------------
Traceback (most recent call last):
 File "test_PopGen_SimCoal_nodepend.py", line 23, in test_template_full
   'PopGen')
 File 
"~/biopython-1.50/build/lib.linux-i686-2.3/Bio/PopGen/SimCoal/Template.py", 
line 210, in generate_simcoal_from_template
   stream = open(out_dir + sep + 'tmp.par', 'w')
IOError: [Errno 13] Permission denied: 'PopGen/tmp.par'

======================================================================
ERROR: test_SeqUtils
----------------------------------------------------------------------
[Errno 13] Permission denied: 'fasta.tmp'
======================================================================

How can I bypass these errors without giving non-root users write 
permission?

Thanks,

Finsen