From 2ee8a406fde6038afd55a827b642d532a27afe4b Mon Sep 17 00:00:00 2001 From: Daniel Date: Wed, 1 May 2019 10:22:53 +0100 Subject: [PATCH] Update FFPred_README Made some updates to the install instructions --- FFPred_README | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/FFPred_README b/FFPred_README index a8a21b7..ffdd995 100644 --- a/FFPred_README +++ b/FFPred_README @@ -18,8 +18,7 @@ pieces of third-party software. This code is capable of running analyses with Human SVMs v3.0 and Fly SVMs v1.0 (see below) Detailed instructions on how to set everything up are reported below. Please - take some time to read them carefully and in sequential order - ignore them - at your peril! + take some time to read them carefully and in sequential order #------------------------------------------------------------------------------ @@ -70,8 +69,9 @@ ITS USE AND ANY RESULTS OBTAINED. SIGNALP http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp WoLFPSORT http://bioinfadmin.cs.ucl.ac.uk/downloads/ffpred_feature_suite/wolfpsort_0.2.zip PFILT http://bioinfadmin.cs.ucl.ac.uk/downloads/pfilt/ - BLAST ftp://ftp.ncbi.nih.gov/blast/executables/ + BLAST ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/ SVM-Light http://svmlight.joachims.org/ + Uniref90 ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz Perl 5.6 or later, including core modules Getopt::Long and Digest::MD5 @@ -95,10 +95,10 @@ ITS USE AND ANY RESULTS OBTAINED. chmod a+x FFPred.pl chmod a+x featurama/features.pl - chmod a+x material/uniref/UniRef_xml_to_fasta.pl Also, make sure the relevant folders can be written to: + mkdir bin data featurama SVMs uniref90 chmod -R u+w bin data featurama SVMs uniref90 chmod a+w jobs chmod a+w out @@ -113,8 +113,8 @@ ITS USE AND ANY RESULTS OBTAINED. perl -c FFPred.pl perl -c featurama/features.pl - Finally, note that the release includes a configuration file, called - "FFPred4/CONFIG", that can be edited to set many useful paths (all of them + Finally, edit the included a configuration file, called + "FFPred4/CONFIG", to set the paths (all of them are explained in detail in what follows): PFILT directory containing the executable for pfilt software @@ -134,7 +134,7 @@ ITS USE AND ANY RESULTS OBTAINED. SEQFEAT directory containing the executable for SeqFeat PEST directory containing the executable for EMBOSS/pestefind software PATH directory for temporary FFPred4 files - DB full path to FASTA database (UniRef90) + DB full path to FASTA database (UniRef90) MASK_DB full path to masked version of FASTA database (UniRef90) Importantly, as explained in the file header, all paths need to be specified @@ -147,6 +147,9 @@ ITS USE AND ANY RESULTS OBTAINED. IMPORTANT: You should ensure each of these packages is installed and working correctly before you attempt to run FFPred. NETPHOS, NETOGLYC, NETNGLYC will all need to be hand edited. + + IMPORTANT: You must ensure that the correct blast database created using the + BLAST formatdb tool #------------------------------------------------------------------------------