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commit 62eb519cf45699ebfbeeb9846c79cc184fe8ab08 Author: Afif Elghraoui <[email protected]> Date: Fri Jan 20 00:36:58 2017 -0800 Add example data --- debian/copyright | 4 ++++ debian/data/pacbio.filtered_subreads.fasta.gz | Bin 0 -> 1438059 bytes debian/examples | 1 + debian/patches/example-specs.patch | 29 ++++++++++++++++++++++++++ debian/patches/series | 1 + debian/source/include-binaries | 1 + 6 files changed, 36 insertions(+) diff --git a/debian/copyright b/debian/copyright index dad768c..ecb465d 100644 --- a/debian/copyright +++ b/debian/copyright @@ -25,6 +25,10 @@ License: BSD-3-Clause Files: debian/* Copyright: 2016 Afif Elghraoui <[email protected]> License: MIT +Comment: + debian/data/* is uncopyrightable data. It was retrieved from the + sample data tarball at + <http://www.cbcb.umd.edu/software/PBcR/data/sampleData.tar.gz>. License: MIT Permission is hereby granted, free of charge, to any person obtaining a diff --git a/debian/data/pacbio.filtered_subreads.fasta.gz b/debian/data/pacbio.filtered_subreads.fasta.gz new file mode 100644 index 0000000..e91e2e3 Binary files /dev/null and b/debian/data/pacbio.filtered_subreads.fasta.gz differ diff --git a/debian/examples b/debian/examples index 4a1cc83..6a83289 100644 --- a/debian/examples +++ b/debian/examples @@ -1,3 +1,4 @@ ec.spec pbasm.spec doc/_build/html/_sources/Example.txt +debian/data/* diff --git a/debian/patches/example-specs.patch b/debian/patches/example-specs.patch new file mode 100644 index 0000000..7a3b1da --- /dev/null +++ b/debian/patches/example-specs.patch @@ -0,0 +1,29 @@ +Description: Configure example/test run + Use the provided example data and disable running wgs-assembler + (which is discontinued upstream anyway). +Author: Afif Elghraoui <[email protected]> +Forwarded: no +Last-Update: 2017-01-19 +--- sprai.orig/ec.spec ++++ sprai/ec.spec +@@ -1,6 +1,6 @@ + #### common #### + # input_for_database: filtered subreads in fasta or fastq format +-input_for_database all.fq ++input_for_database pacbio.filtered_subreads.fasta + + # min_len_for_query: the subreads longer than or equal to this value will be corrected + min_len_for_query 500 +@@ -11,9 +11,9 @@ + estimated_depth 100 + + # ca_path: where Celera Assembler exist in +-# If you don't have it and only want to run error-correction, +-# don't set this variable (comment it out) +-ca_path /home/imai/wgs/Linux-amd64/bin/ ++# If have it and want to run a full assembly with it, ++# set this variable ++# ca_path /home/imai/wgs/Linux-amd64/bin/ + + # the number of processes used by all vs. all alignment + # = 'partition' (in single node mode) diff --git a/debian/patches/series b/debian/patches/series index 29dab71..e7bfaa1 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1 +1,2 @@ libexec.patch +example-specs.patch diff --git a/debian/source/include-binaries b/debian/source/include-binaries new file mode 100644 index 0000000..9a5803b --- /dev/null +++ b/debian/source/include-binaries @@ -0,0 +1 @@ +debian/data/pacbio.filtered_subreads.fasta.gz -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/sprai.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
