[med-svn] [Git][med-team/t-coffee][master] 2 commits: Remove un-needed patch

[Nilesh Patra]

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 <chuprikovalv at gmail.com> 
-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
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