Nilesh Patra pushed to branch master at Debian Med / t-coffee
Commits: f29b7300 by Nilesh Patra at 2020-04-16T16:00:32+05:30 Remove un-needed patch - - - - - 349ea6cd by Nilesh Patra at 2020-04-16T16:00:56+05:30 Adapt tests with new version - - - - - 3 changed files: - − debian/patches/fix_tempfile_name_sharing.patch - debian/patches/series - debian/tests/run-unit-test Changes: ===================================== debian/patches/fix_tempfile_name_sharing.patch deleted ===================================== @@ -1,18 +0,0 @@ -Author: Liubov Chuprikova <[email protected]> -Bug-Debian: https://bugs.debian.org/917143 -Last-Update: Sun, 03 Feb 2019 23:42:41 +0100 -Description: Delete static for tempfile names so that -different processes do not use the same file. - - ---- a/t_coffee_source/util_lib/reformat.c -+++ b/t_coffee_source/util_lib/reformat.c -@@ -6201,6 +6201,8 @@ Alignment * read_gotoh_aln ( char *fname - } - } - -+ vfree(tmp_name1); -+ vfree(tmp_name2); - } - - vfclose (fp); ===================================== debian/patches/series ===================================== @@ -6,5 +6,4 @@ set_proper_dir_permissions.patch mayhem.patch stable-linking-inputs.patch clustalw2.patch -fix_tempfile_name_sharing.patch verbose_build ===================================== debian/tests/run-unit-test ===================================== @@ -15,26 +15,25 @@ find . -name "*.gz" -exec gunzip \{\} \; # Make sure HOME is set in environment (see bug #909530) export HOME=${HOME:-$PWD} -t_coffee sample_seq1.fasta -t_coffee sample_seq1.fasta -mode quickaln -t_coffee sample_seq1.fasta -mode quickaln -ndiag=10 -t_coffee -aln=sproteases_small.cw_aln, sproteases_small.muscle, sproteases_small.tc_aln -outfile=combined_aln.aln -t_coffee -infile=sproteases_small.aln -special_mode=evaluate -t_coffee -other_pg seq_reformat -in sproteases_small.aln -output fasta_aln > sproteases_small.fasta_aln -t_coffee -other_pg seq_reformat -in sproteases_small.aln -output msf > sproteases_small.msf -t_coffee -other_pg seq_reformat -in sproteases_small.aln -output fasta_seq > sproteases_small.fasta -t_coffee -other_pg seq_reformat -in sproteases_small.aln -action +lower -output clustalw -t_coffee -other_pg seq_reformat -in sample_aln1.aln -action +upper +edit_residue hmgb_chite 10 lower -t_coffee -other_pg seq_reformat -in sample_aln1.aln -in3 sample_aln1.aln -action +upper +3evaluate idmat +lower '' -t_coffee -other_pg seq_reformat -in sproteases_large.fasta -output code_name > sproteases_large.code_name -t_coffee -other_pg seq_reformat -code sproteases_large.code_name -in sproteases_large.fasta >sproteases_large.coded.fasta -t_coffee -other_pg seq_reformat -decode sproteases_large.code_name -in sproteases_large.coded.fasta -t_coffee -other_pg seq_reformat -in sample_aln1.aln -in3 sample_aln1.aln -action +3convert a0 -output color_html > colored.html -t_coffee -other_pg seq_reformat -in sample_aln1.aln -action +color_residue hmgb_chite 10 1 -output color_html > color.html -t_coffee -other_pg seq_reformat -in sample_aln1.aln -in3 sample_aln1.aln -action +3evaluate pam250mt -output color_html > color.html -t_coffee -other_pg seq_reformat -in sample_aln1.aln -in3 sample_aln1.aln -action +3evaluate boxshade -output color_html > color.html -t_coffee -other_pg seq_reformat -in=sample_aln6.aln -output=clustalw_aln -out=cache.aln -action +convert 'Aa1' '.--' +convert '#0' -t_coffee -other_pg seq_reformat -in=sample_aln6.aln -output=fasta_seq -out=cache.seq -action +convert 'Aa1' '.--' +convert '#0' -t_coffee -other_pg seq_reformat -in=sample_aln6.aln -output=fasta_seq -out=cache -action +convert 'Aa1' '.--' -t_coffee -other_pg seq_reformat -in=sample_aln6.aln -struc_in=sample_aln6.cache -struc_in_f number_fasta -output=color_html -out=x.html - +t_coffee sample_rnaseq1.fasta +t_coffee sample_rnaseq1.fasta -mode quickaln +t_coffee sample_rnaseq1.fasta -mode quickaln -ndiag=10 +t_coffee proteases_small.fasta -aln g0.aln g5.aln g10.aln g15.aln -output=clustalw,html +t_coffee -infile=sample_aln1.aln -lib=sample_aln1.tc_lib -special_mode=evaluate +t_coffee -other_pg seq_reformat -in proteases_small.aln -output fasta_aln > proteases_small.fasta_aln +t_coffee -other_pg seq_reformat -in proteases_small.aln -output msf > proteases_small.msf +t_coffee -other_pg seq_reformat -in proteases_small.aln -output fasta_seq > proteases_small.fasta +t_coffee -other_pg seq_reformat -in proteases_small.aln -action +lower -output clustalw +t_coffee -other_pg seq_reformat -in sample_aln1.aln -action +upper +edit_residue hmgb_chite 10 lower +t_coffee -other_pg seq_reformat -in sample_aln1.aln -in3 sample_aln1.aln -action +upper +3evaluate idmat +lower '' +t_coffee -other_pg seq_reformat -in proteases_large.fasta -output code_name > proteases_large.code_name +t_coffee -other_pg seq_reformat -code proteases_large.code_name -in proteases_large.fasta >proteases_large.coded.fasta +t_coffee -other_pg seq_reformat -decode proteases_large.code_name -in proteases_large.coded.fasta +t_coffee -other_pg seq_reformat -in sample_aln1.aln -in3 sample_aln1.aln -action +3convert a0 -output color_html > colored.html +t_coffee -other_pg seq_reformat -in sample_aln1.aln -action +color_residue hmgb_chite 10 1 -output color_html > color.html +t_coffee -other_pg seq_reformat -in sample_aln1.aln -in3 sample_aln1.aln -action +3evaluate pam250mt -output color_html > color.html +t_coffee -other_pg seq_reformat -in sample_aln1.aln -in3 sample_aln1.aln -action +3evaluate boxshade -output color_html > color.html +t_coffee -other_pg seq_reformat -in=sample_dnaseq2.aln -output=clustalw_aln -out=cache.aln -action +convert 'Aa1' '.--' +convert '#0' +t_coffee -other_pg seq_reformat -in=sample_dnaseq2.aln -output=fasta_seq -out=cache.seq -action +convert 'Aa1' '.--' +convert '#0' +t_coffee -other_pg seq_reformat -in=sample_dnaseq2.aln -output=fasta_seq -out=cache -action +convert 'Aa1' '.--' +t_coffee -other_pg seq_reformat -in=sample_dnaseq2.aln -struc_in=sample_dnaseq2.cache -struc_in_f number_fasta -output=color_html -out=x.html View it on GitLab: https://salsa.debian.org/med-team/t-coffee/-/compare/c2aee3eedc05bcc2dc3ac06cea52fa3e34305cca...349ea6cd9a3cec163ef5d157ad111e3fbceaa24d -- View it on GitLab: https://salsa.debian.org/med-team/t-coffee/-/compare/c2aee3eedc05bcc2dc3ac06cea52fa3e34305cca...349ea6cd9a3cec163ef5d157ad111e3fbceaa24d You're receiving this email because of your account on salsa.debian.org.
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