Description: fix interpreter paths
 Make Perl paths compliant with the policy.
Author: Sascha Steinbiss <satta@debian.org>
Last-Update: 2019-09-18
--- a/scripts/aa2nonred.pl
+++ b/scripts/aa2nonred.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # take a multiple fasta amino acid sequence file
 # and output a file that is non-redundant:
--- a/scripts/augustus2browser.pl
+++ b/scripts/augustus2browser.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # This takes the AUGUSTUS output in the standard input
 # and outputs to standard output a file with UCSC browser gtf format
--- a/scripts/augustus2gbrowse.pl
+++ b/scripts/augustus2gbrowse.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 # convert AUGUSTUS output to Gbrowse format GFF file
 # Mario Stanke
 
--- a/scripts/autoAug.pl
+++ b/scripts/autoAug.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 
 ##########################################################################################################################
--- a/scripts/autoAugPred.pl
+++ b/scripts/autoAugPred.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 
 ##########################################################################################################################
--- a/scripts/autoAugTrain.pl
+++ b/scripts/autoAugTrain.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 
 ###########################################################################################################################
--- a/scripts/bedgraph2wig.pl
+++ b/scripts/bedgraph2wig.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 use strict;
 use warnings;
 use Getopt::Long;
--- a/scripts/blat2gbrowse.pl
+++ b/scripts/blat2gbrowse.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # convert a blat output file (tab format) for transcript alignments
 # to a GBrowse GFF file and the multiple fasta file with the matching ests
--- a/scripts/blat2hints.pl
+++ b/scripts/blat2hints.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # Convert a psl format output file (from BLAT or GMAP) from cDNA alignments
 # to a hints file
--- a/scripts/block2prfl.pl
+++ b/scripts/block2prfl.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 ################################################################################
 #
 #   Name:    block2prfl.pl
--- a/scripts/cegma2gff.pl
+++ b/scripts/cegma2gff.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # Katharina J. Hoff, May 26th 2015
 #
--- a/scripts/checkParamArchive.pl
+++ b/scripts/checkParamArchive.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # This script checks whether a parameter *.tar.gz archive contains valid AUGUSTUS parameter files. Errors due to missing files are written to STDERR. If UTR parameters are not present, this is written to STDOUT.
 # param-archive.tar.gz is the archive in question
--- a/scripts/cleanDOSfasta.pl
+++ b/scripts/cleanDOSfasta.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # "Clean" a MS/DOS fasta file from weird characters that screw with e.g. Perl
 
--- a/scripts/clusterAndSplitGenes.pl
+++ b/scripts/clusterAndSplitGenes.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # read in a file with inter-gene dependencies and
 # create clusters without inter-cluster dependencies
--- a/scripts/computeFlankingRegion.pl
+++ b/scripts/computeFlankingRegion.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # Authors: Katharina Hoff & Sophie Kersting
 # Contact: katharina.hoff@uni-greifswald.de
--- a/scripts/createAugustusJoblist.pl
+++ b/scripts/createAugustusJoblist.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # createAugustusJoblist.pl
 # Create a joblist with overlapping sequence chunks from multiple fasta files.
--- a/scripts/del_from_prfl.pl
+++ b/scripts/del_from_prfl.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 use strict;
 use warnings;
 
--- a/scripts/evalCGP.pl
+++ b/scripts/evalCGP.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ###################################################################################################
 # evalCGP
--- a/scripts/eval_dualdecomp.pl
+++ b/scripts/eval_dualdecomp.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 use strict;
 use warnings;
--- a/scripts/eval_multi_gtf.pl
+++ b/scripts/eval_multi_gtf.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # compute the accuracy values of a set of predictions
 # against a set of annotations
--- a/scripts/exonerate2hints.pl
+++ b/scripts/exonerate2hints.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # generate hints from an Exonerate gff dump
 # Mario Stanke June, 2007
--- a/scripts/exoniphyDb2hints.pl
+++ b/scripts/exoniphyDb2hints.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 #  convert the exoniphy exon predictions to a file with hints to AUGUSTUS
 #
--- a/scripts/extractTranscriptEnds.pl
+++ b/scripts/extractTranscriptEnds.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # extract transcript ends of a given length from a gene fasta file (no UTR)
 # Katharina Hoff, 9.8.2011, katharina.hoff@gmail.com
--- a/scripts/filterGenesIn_mRNAname.pl
+++ b/scripts/filterGenesIn_mRNAname.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 #############################################################################
 # filterGenesIn_mRNAname.pl
--- a/scripts/filterGenesIn.pl
+++ b/scripts/filterGenesIn.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ##############################################################
 # filterGenes
--- a/scripts/filterGenesOut_mRNAname.pl
+++ b/scripts/filterGenesOut_mRNAname.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 #############################################################
 # filterGenes
--- a/scripts/filterGenes.pl
+++ b/scripts/filterGenes.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 #############################################################
 # filterGenes
--- a/scripts/filterInFrameStopCodons.pl
+++ b/scripts/filterInFrameStopCodons.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # Katharina J. Hoff
 # March 5th 2012
--- a/scripts/filterMaf.pl
+++ b/scripts/filterMaf.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 # filter blocks from a MAF alignment that intersect with a given genomic interval
 # or filter sequences for a given subset of species
 # Stefanie Koenig 23.06.2013
--- a/scripts/filter-ppx.pl
+++ b/scripts/filter-ppx.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 use strict;
 use warnings;
--- a/scripts/filterPSL.pl
+++ b/scripts/filterPSL.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # filter a psl file (from BLAT,GMAP)
 #
--- a/scripts/filterShrimp.pl
+++ b/scripts/filterShrimp.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # filter a file from the Shrimp alignment program
 #
--- a/scripts/filterSpliceHints.pl
+++ b/scripts/filterSpliceHints.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # filter augustus splice hints file (e.g. from RNA-seq data)
 # for splice hints that contain a particular splicing motif,
--- a/scripts/findGffNamesInFasta.pl
+++ b/scripts/findGffNamesInFasta.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # Author: Katharina J. Hoff
 # Date: Oct. 27 2017
--- a/scripts/fix_joingenes_gtf.pl
+++ b/scripts/fix_joingenes_gtf.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ####################################################################################################
 #                                                                                                  #
--- a/scripts/gbrowseold2gff3.pl
+++ b/scripts/gbrowseold2gff3.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 # convert old gbrowse format of gene predictions to gff3 format
 # Mario Stanke, 3/8/2011, mario.stanke@uni-greifswald.de
 
--- a/scripts/gbSmallDNA2gff.pl
+++ b/scripts/gbSmallDNA2gff.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # create a genome-scale gff file from a gb file that created for AUGUSTUS training (has a flanking region, coordinates of the origin of sequence are given in the LOCUS tag)
 #
--- a/scripts/getAnnoFasta.pl
+++ b/scripts/getAnnoFasta.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # getAnnoFast.pl
 # Creates fasta sequence files from the AUGUSTUS output.
--- a/scripts/getLinesMatching.pl
+++ b/scripts/getLinesMatching.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # Author: Mario Stanke
 # Contact: mario.stanke@uni-greifswald.de
--- a/scripts/gffGetmRNA.pl
+++ b/scripts/gffGetmRNA.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 # gffGetmRNA.pl
 # Creates mRNA fasta sequence files from a GFF with gene annotation
 # 
--- a/scripts/gp2othergp.pl
+++ b/scripts/gp2othergp.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # convert genepred format from UCSC gtfToGenePred -genePredExt
 # table genePredExt
--- a/scripts/gtf2aa.pl
+++ b/scripts/gtf2aa.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # Convert a gtf file and corresponding genome fasta file to protein file with standard translational code
 # Katharina J. Hoff
--- a/scripts/gtf2bed.pl
+++ b/scripts/gtf2bed.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # convert gtf/gff/gff3 to BED format
 # 23.9.2016 Stefanie Koenig
--- a/scripts/gtf2gff.pl
+++ b/scripts/gtf2gff.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # format convert a gtf file
 #
--- a/scripts/gth2gtf.pl
+++ b/scripts/gth2gtf.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # Authors: Katharina Hoff
 # Contact: katharina.hoff@uni-greifswald.de
--- a/scripts/hal2maf_split.pl
+++ b/scripts/hal2maf_split.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 # this script works on top of the 'halTools' toolbox
 # and exports a hal alignment to maf by splitting the alignment into several smaller
 # alignment chunks of a certain size. An overlap between two consecutive alignment chunks can
--- a/scripts/join_aug_pred.pl
+++ b/scripts/join_aug_pred.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # join_aug_pred.pl
 # Join AUGUSTUS predictions from separate runs of possibly overlapping sequence segments.
--- a/scripts/join_mult_hints.pl
+++ b/scripts/join_mult_hints.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # summarize multiple identical hints to one with mult=n
 #
--- a/scripts/joinPeptides.pl
+++ b/scripts/joinPeptides.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # Creates a fasta file with unique peptides from two peptide fasta input files
 # Deletes redundant entries. Multiplicity information is taken from the first
--- a/scripts/maf2conswig.pl
+++ b/scripts/maf2conswig.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # Convert maf alignment format to a conservation graph in wig format
 # Use simply average percentage of identity in a sliding window as VISTA does.
--- a/scripts/makeMatchLists.pl
+++ b/scripts/makeMatchLists.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # make for each matching est contig a list of matching genomic contigs in the same line
 #
--- a/scripts/makeUtrTrainingSet.pl
+++ b/scripts/makeUtrTrainingSet.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # Construct likely UTR regions from EST alignments and codon region boundaries
 # e.g. to make a training set to train the AUGUSTUS UTR models.
--- a/scripts/maskNregions.pl
+++ b/scripts/maskNregions.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # create a gff-like file that marks regions in a fasta file
 # that contain "N" or "n".
--- a/scripts/moveParameters.pl
+++ b/scripts/moveParameters.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # Katharina J. Hoff & Henry Mehlan
 # last modified on January 24th 2019
--- a/scripts/msa2prfl.pl
+++ b/scripts/msa2prfl.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 ################################################################################
 #
 #   Name:    msa2prfl.pl
--- a/scripts/new_species.pl
+++ b/scripts/new_species.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # This script is used by the braker.pl pipeline.
 # Please be extremely careful when changing this script because the braker.pl
--- a/scripts/optimize_augustus.pl
+++ b/scripts/optimize_augustus.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ##################################################################################
 # optimize_augustus
--- a/scripts/opt_init_and_term_probs.pl
+++ b/scripts/opt_init_and_term_probs.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 #############################################################
 # opt_init_and_term_probs.pl
--- a/scripts/parseSim4Output.pl
+++ b/scripts/parseSim4Output.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # parse the output of sim4, fiter the alignments and
 # output them to stdout
--- a/scripts/partition_gtf2gb.pl
+++ b/scripts/partition_gtf2gb.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # Partition a gff file into gene clusters of a specified minimal number of genes,
 # clusters shall not end in another gene.
--- a/scripts/pasapolyA2hints.pl
+++ b/scripts/pasapolyA2hints.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/bin env
+#!/usr/bin/perl
 use strict;
 use warnings;
 use Getopt::Long;
--- a/scripts/peptides2alternatives.pl
+++ b/scripts/peptides2alternatives.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # Katharina J. Hoff, Jan 30th 2012
 #
--- a/scripts/peptides2hints.pl
+++ b/scripts/peptides2hints.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # Katharina J. Hoff
 # January 2012
--- a/scripts/phastconsDB2hints.pl
+++ b/scripts/phastconsDB2hints.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # convert phastcons track to a file with hints to AUGUSTUS
 # 
--- a/scripts/polyA2hints.pl
+++ b/scripts/polyA2hints.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # Convert a polyA polyT position table to tts hints
 # This is for the polyA/T tables from Chun Liang
--- a/scripts/prints2prfl.pl
+++ b/scripts/prints2prfl.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 ################################################################################
 #
 #   Name:    prints2prfl.pl
--- a/scripts/pslMap.pl
+++ b/scripts/pslMap.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 # combine two psl files transitively
 # 
 #     map target (genome)
--- a/scripts/randomSplit.pl
+++ b/scripts/randomSplit.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ##############################################################################
 # randomSplit
--- a/scripts/retroDB2hints.pl
+++ b/scripts/retroDB2hints.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 #  convert the retroGenes track to a file with hints to AUGUSTUS
 #
--- a/scripts/rmRedundantHints.pl
+++ b/scripts/rmRedundantHints.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # Katharina J. Hoff, Jan 30th 2012
 #
--- a/scripts/runAllSim4.pl
+++ b/scripts/runAllSim4.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # run sim4 once for each line in the matchlist file 
 # 
--- a/scripts/samMap.pl
+++ b/scripts/samMap.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # Map a sam file that was created by aligning against an exon-exon junction file back to genome level.
 # Filters out non-intron-containing alignments.
--- a/scripts/scipiogff2gff.pl
+++ b/scripts/scipiogff2gff.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # convert a gff from scipio to a gff file in a format that
 # can then be converted to genbank, e.g. with gff2gbSmallDNA.pl
--- a/scripts/setStopCodonFreqs.pl
+++ b/scripts/setStopCodonFreqs.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 # Author: Katharina J. Hoff
 # Date: February 19th 2018
 # set stop codon frequencies in parameters.cfg of a particular species
--- a/scripts/simpleFastaHeaders.pl
+++ b/scripts/simpleFastaHeaders.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # Katharina J. Hoff, May 5th 2011
 #
--- a/scripts/simplifyFastaHeaders.pl
+++ b/scripts/simplifyFastaHeaders.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # Katharina J. Hoff, Dec 3rd 2012
 #
--- a/scripts/splitMfasta.pl
+++ b/scripts/splitMfasta.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # splitMfasta.pl
 # split a multiple fasta file in smaller multiple fasta files
--- a/scripts/split_wiggle.pl
+++ b/scripts/split_wiggle.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # split a wiggle file in single contig files
 
--- a/scripts/summarizeACGTcontent.pl
+++ b/scripts/summarizeACGTcontent.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 use strict;
 use warnings;
 
--- a/scripts/transMap2hints.pl
+++ b/scripts/transMap2hints.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # Mario Stanke, 26.01.2007
 # convert a transmap output file (tab format) to a hints file
--- a/scripts/uniquePeptides.pl
+++ b/scripts/uniquePeptides.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # Creates a fasta file with unique peptides from a fasta input file
 # where identical peptide match multiple positions. The first found 
--- a/scripts/utrgff2gbrowse.pl
+++ b/scripts/utrgff2gbrowse.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 # convert a utr.gff from makeUtrTrainingSet.pl to a gbrowse file
 # Mario Stanke, 9.4.2008
 #
--- a/scripts/weedMaf.pl
+++ b/scripts/weedMaf.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # weedMaf remove only-gap columns from a multiple alignment in MAF format
 #
--- a/scripts/wig2hints.pl
+++ b/scripts/wig2hints.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # wig2hints.pl
 #
--- a/scripts/wigchoose.pl
+++ b/scripts/wigchoose.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # choose an interval with good coverage
 #
--- a/scripts/writeResultsPage.pl
+++ b/scripts/writeResultsPage.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # This scripts writes an HTML results page and does all the necessary file modifications for making results of the AUGUSTUS training web server application available.
 
--- a/scripts/yaml2gff.1.4.pl
+++ b/scripts/yaml2gff.1.4.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 ################################################################################
 #
 #   Project: Gene Prediction with Protein Family Patterns 
--- a/scripts/add_name_to_gff3.pl
+++ b/scripts/add_name_to_gff3.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # add name of feature to a gff3 file that produced by gtf2gff.pl from Augustus/scripts
 #
--- a/scripts/compare_masking.pl
+++ b/scripts/compare_masking.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # Katharina J. Hoff
 # November 20th 2018
--- a/scripts/get_loci_from_gb.pl
+++ b/scripts/get_loci_from_gb.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 ####################################################################################################
 #                                                                                                  #
--- a/scripts/gff2gbSmallDNA.pl
+++ b/scripts/gff2gbSmallDNA.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 #
 # This script is used by the braker.pl pipeline.
 # Please be extremely careful when changing this script because the braker.pl
--- a/scripts/merge_masking.pl
+++ b/scripts/merge_masking.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 # Katharina J. Hoff
 # November 20th 2018
--- a/scripts/augustify.py
+++ b/scripts/augustify.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
 
 import os
 import errno
--- a/scripts/bamToWig.py
+++ b/scripts/bamToWig.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
 
 # Convert bam files to wiggle files for usage with AUGUSTUS (exonpart hints)
 # Alternative to Augustus/auxprogs/bam2wig/bam2wig, which often causes
--- a/scripts/extractAnno.py
+++ b/scripts/extractAnno.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
 import argparse
 import fileinput
 import sys
--- a/scripts/fix_in_frame_stop_codon_genes.py
+++ b/scripts/fix_in_frame_stop_codon_genes.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
 
 # Author: Anica Hoppe
 # Last modified: March 25th 2020
--- a/scripts/getAnnoFastaFromJoingenes.py
+++ b/scripts/getAnnoFastaFromJoingenes.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python3
+#!/usr/bin/python3
 
 # Author: Katharina J. Hoff
 # E-Mail: katharina.hoff@uni-greifswald.de
--- a/docs/tutorial/data/gff2browser.pl
+++ b/docs/tutorial/data/gff2browser.pl
@@ -1,4 +1,4 @@
-#!/usr/bin/env perl
+#!/usr/bin/perl
 
 use strict;
 use warnings;