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commit ce6d9b7066f303311c8e45db322981dc306ed350 Author: Olivier Sallou <[email protected]> Date: Sat Jan 14 08:03:11 2017 +0000 include examples --- debian/dirs | 1 + debian/patches/adapt_examples.patch | 25 +++++++++++++++++++++++++ debian/patches/series | 1 + debian/rules | 6 ++++-- 4 files changed, 31 insertions(+), 2 deletions(-) diff --git a/debian/dirs b/debian/dirs index e772481..b4c3671 100644 --- a/debian/dirs +++ b/debian/dirs @@ -1 +1,2 @@ usr/bin +usr/share/doc/baitfisher/example/BaitFisher-results diff --git a/debian/patches/adapt_examples.patch b/debian/patches/adapt_examples.patch new file mode 100644 index 0000000..38806cd --- /dev/null +++ b/debian/patches/adapt_examples.patch @@ -0,0 +1,25 @@ +Subject: update example command to match debian binary +Description: in Debian, binary does not contain version name, + use base name and exec in PATH +Author: Olivier Sallou <[email protected]> +Last-Updated: 2017-01-14 +Forwarded: no +--- a/Example/Example-without-alignment-cutting/run-command ++++ b/Example/Example-without-alignment-cutting/run-command +@@ -1 +1 @@ +-../../BaitFisher-v1.2.7 parameter.txt 1> console_output 2> console_error_output ++BaitFisher parameter.txt 1> console_output 2> console_error_output +--- a/Example/Example-without-alignment-cutting/BaitFilter-analysis/run-BaitFilter ++++ b/Example/Example-without-alignment-cutting/BaitFilter-analysis/run-BaitFilter +@@ -1,6 +1,6 @@ +-../../../BaitFilter-v1.0.5 -m ab -i ../BaitFisher-results/loci_baits.txt -o baits_filtered_best-in-alignment_minNumBaits.txt 1> console_o_filter_bestBaits 2> console_e_filter_bestBaits +-../../../BaitFilter-v1.0.5 -m as -i ../BaitFisher-results/loci_baits.txt -o baits_filtered_best-in-alignment_maxNumSeq.txt 1> console_o_filter_bestSeqs 2> console_e_filter_bestSeqs ++BaitFilter -m ab -i ../BaitFisher-results/loci_baits.txt -o baits_filtered_best-in-alignment_minNumBaits.txt 1> console_o_filter_bestBaits 2> console_e_filter_bestBaits ++BaitFilter -m as -i ../BaitFisher-results/loci_baits.txt -o baits_filtered_best-in-alignment_maxNumSeq.txt 1> console_o_filter_bestSeqs 2> console_e_filter_bestSeqs + + ## Produce bait file that can be uploaded at a bait producing company. So war all companies accepted the file produced with the following command. +-../../../BaitFilter-v1.0.5 -c Agilent-Germany -i baits_filtered_best-in-alignment_maxNumSeq.txt -o Final_baits_filtered_best-in-alignment_maxNumSeq.txt --ID-prefix My-project-name- 1> conversion_maxNumSeq.o 2> conversion_maxNumSeq.e +-../../../BaitFilter-v1.0.5 -c Agilent-Germany -i baits_filtered_best-in-alignment_minNumBaits.txt -o Final_baits_filtered_best-in-alignment_minNumBaits.txt --ID-prefix My-project-name- 1> conversion_minNumBaits.o 2> conversion_minNumBaits.e +\ No newline at end of file ++BaitFilter -c Agilent-Germany -i baits_filtered_best-in-alignment_maxNumSeq.txt -o Final_baits_filtered_best-in-alignment_maxNumSeq.txt --ID-prefix My-project-name- 1> conversion_maxNumSeq.o 2> conversion_maxNumSeq.e ++BaitFilter -c Agilent-Germany -i baits_filtered_best-in-alignment_minNumBaits.txt -o Final_baits_filtered_best-in-alignment_minNumBaits.txt --ID-prefix My-project-name- 1> conversion_minNumBaits.o 2> conversion_minNumBaits.e diff --git a/debian/patches/series b/debian/patches/series index ac462d5..1390f96 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1 +1,2 @@ +adapt_examples.patch fix_gcc6.patch diff --git a/debian/rules b/debian/rules index 5def6d3..25dbe1b 100755 --- a/debian/rules +++ b/debian/rules @@ -13,7 +13,7 @@ include /usr/share/dpkg/pkg-info.mk dh $@ override_dh_install: - cp BaitFilter-v* debian/baitfisher/usr/bin/BaitFiler + cp BaitFilter-v* debian/baitfisher/usr/bin/BaitFilter cp BaitFisher-v* debian/baitfisher/usr/bin/BaitFisher dh_install @@ -22,5 +22,7 @@ override_dh_installman: help2man --no-discard-stderr -o BaitFisher.1 ./BaitFisher-v* dh_installman - +override_dh_installdocs: + cp -r Example/* usr/share/doc/baitfisher/example/ + dh_installdocs -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/baitfisher.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
