[med-svn] [sprai] 01/06: Add example data

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository sprai.

commit 62eb519cf45699ebfbeeb9846c79cc184fe8ab08
Author: Afif Elghraoui <afif at debian.org>
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 <afif at debian.org>
 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 <afif at debian.org>
+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

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