Mercurial > repos > greg > phylogenomics_analysis
changeset 35:01c89742cb39 draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 12 Jan 2017 10:00:28 -0500 |
| parents | 8529a3c95c2b |
| children | c42769258e0d |
| files | phylogenomics_analysis.xml |
| diffstat | 1 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/phylogenomics_analysis.xml Thu Jan 12 09:45:01 2017 -0500 +++ b/phylogenomics_analysis.xml Thu Jan 12 10:00:28 2017 -0500 @@ -144,19 +144,19 @@ #end if #end if - && echo "Sequence alignments and corresponding phylogenies: `ls $src_fasta_dir | wc -l` files" > $output_fasta - && ls $src_fasta_dir >> $output_fasta + && echo "Sequence alignments and corresponding phylogenies: `ls $src_fasta_dir | grep f | wc -l` files" > $output_fasta + && ls -al $src_fasta_dir | grep f >> $output_fasta && mv $src_fasta_dir/* $dest_fasta_dir #if $generate_output_aln: - && echo "Multiple sequence alignments using method '$multiple_sequence_alignments_option': `ls $src_aln_dir | wc -l` files" > $output_aln - && ls $src_aln_dir >> $output_aln + && echo "Multiple sequence alignments using method '$multiple_sequence_alignments_option': `ls $src_aln_dir | grep f | wc -l` files" > $output_aln + && ls -al $src_aln_dir | grep f >> $output_aln && mv $src_aln_dir/* $dest_aln_dir #end if #if $generate_output_tree: - && echo "Phylogenetic trees: `ls $src_tree_dir | wc -l` files" > $output_tree - && ls $src_tree_dir >> $output_tree + && echo "Phylogenetic trees (note that some files may be empty): `ls $src_tree_dir | grep f | wc -l` files" > $output_tree + && ls -al $src_tree_dir | grep f >> $output_tree && mv $src_tree_dir/* $dest_tree_dir #end if ]]>