Package: fasta3 / 36.3.8h.2020-02-11-4~0exp0simde

Metadata

Package Version Patches format
fasta3 36.3.8h.2020-02-11-4~0exp0simde 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
Makefile.patch | (download)

make/Makefile | 5 3 + 2 - 0 !
make/Makefile.linux | 4 2 + 2 - 0 !
make/Makefile.linux32 | 4 2 + 2 - 0 !
make/Makefile.linux32_sse2 | 4 2 + 2 - 0 !
make/Makefile.linux64 | 8 4 + 4 - 0 !
make/Makefile.linux64_sse2 | 5 3 + 2 - 0 !
make/Makefile.pcom_t | 8 4 + 4 - 0 !
7 files changed, 20 insertions(+), 18 deletions(-)

 makefile
simde | (download)

src/global_sse2.c | 3 2 + 1 - 0 !
src/glocal_sse2.c | 3 2 + 1 - 0 !
src/smith_waterman_sse2.c | 3 2 + 1 - 0 !
3 files changed, 6 insertions(+), 3 deletions(-)

 fix compiling on non x86 with simd everywhere
local_tests | (download)

test/test.sh | 116 58 + 58 - 0 !
test/test2G.sh | 112 56 + 56 - 0 !
2 files changed, 114 insertions(+), 114 deletions(-)

 disable tests that require external databases

adjust scripts | (download)

psisearch2/clustal2fasta.pl | 2 1 + 1 - 0 !
psisearch2/clustal2fasta.py | 2 1 + 1 - 0 !
psisearch2/m89_btop_msa2.pl | 2 1 + 1 - 0 !
psisearch2/psisearch2_msa.pl | 4 2 + 2 - 0 !
psisearch2/psisearch2_msa.py | 10 5 + 5 - 0 !
psisearch2/psisearch2_msa_iter.sh | 4 2 + 2 - 0 !
psisearch2/psisearch2_msa_iter_bl.sh | 2 1 + 1 - 0 !
scripts/ann_exons_all.pl | 2 1 + 1 - 0 !
scripts/ann_exons_ens.pl | 2 1 + 1 - 0 !
scripts/ann_exons_ncbi.pl | 2 1 + 1 - 0 !
scripts/ann_exons_up_sql.pl | 2 1 + 1 - 0 !
scripts/ann_exons_up_sql_www.pl | 2 1 + 1 - 0 !
scripts/ann_exons_up_www.pl | 2 1 + 1 - 0 !
scripts/ann_feats2ipr.pl | 2 1 + 1 - 0 !
scripts/ann_feats2ipr_e.pl | 2 1 + 1 - 0 !
scripts/ann_feats_up_sql.pl | 2 1 + 1 - 0 !
scripts/ann_feats_up_www2.pl | 2 1 + 1 - 0 !
scripts/ann_ipr_www.pl | 2 1 + 1 - 0 !
scripts/ann_pdb_cath.pl | 2 1 + 1 - 0 !
scripts/ann_pdb_vast.pl | 2 1 + 1 - 0 !
scripts/ann_pfam30_tmptbl.pl | 2 1 + 1 - 0 !
scripts/ann_pfam_sql.pl | 2 1 + 1 - 0 !
scripts/ann_pfam_www.pl | 2 1 + 1 - 0 !
scripts/ann_script_list | 16 7 + 9 - 0 !
scripts/ann_upfeats_pfam_www_e.pl | 2 1 + 1 - 0 !
scripts/annot_blast_btop2.pl | 2 1 + 1 - 0 !
scripts/annot_blast_btop3.py | 2 1 + 1 - 0 !
scripts/annot_blast_btop4.py | 2 1 + 1 - 0 !
scripts/blastp_annot_cmd.sh | 6 3 + 3 - 0 !
scripts/blastp_cmd.sh | 2 1 + 1 - 0 !
scripts/exp_up_ensg.pl | 2 1 + 1 - 0 !
scripts/expand_links.pl | 2 1 + 1 - 0 !
scripts/expand_refseq_isoforms.pl | 2 1 + 1 - 0 !
scripts/expand_uniref50.pl | 2 1 + 1 - 0 !
scripts/expand_up_isoforms.pl | 2 1 + 1 - 0 !
scripts/fasta_annot_cmd.sh | 6 3 + 3 - 0 !
scripts/get_genome_seq.py | 2 1 + 1 - 0 !
scripts/get_protein.py | 2 1 + 1 - 0 !
scripts/get_protein_sql.py | 2 1 + 1 - 0 !
scripts/get_protein_sql_www.py | 2 1 + 1 - 0 !
scripts/get_refseq.py | 2 1 + 1 - 0 !
scripts/get_uniprot.py | 2 1 + 1 - 0 !
scripts/get_up_prot_iso_sql.py | 2 1 + 1 - 0 !
scripts/lav2plt.pl | 2 1 + 1 - 0 !
scripts/lavplt_ps.pl | 2 1 + 1 - 0 !
scripts/lavplt_svg.pl | 2 1 + 1 - 0 !
scripts/links2sql.pl | 2 1 + 1 - 0 !
scripts/m8_btop_msa.pl | 2 1 + 1 - 0 !
scripts/m9B_btop_msa.pl | 2 1 + 1 - 0 !
scripts/map_exon_coords.py | 2 1 + 1 - 0 !
scripts/merge_blast_btab.pl | 2 1 + 1 - 0 !
scripts/merge_fasta_btab.pl | 2 1 + 1 - 0 !
scripts/relabel_domains.py | 2 1 + 1 - 0 !
scripts/rename_exons.py | 2 1 + 1 - 0 !
scripts/summ_domain_ident.pl | 2 1 + 1 - 0 !
scripts/test_ann_scripts.sh | 22 11 + 11 - 0 !
scripts/test_py.sh | 67 34 + 33 - 0 !
57 files changed, 116 insertions(+), 117 deletions(-)

 adjust for installed use