New Upstream Snapshot - megahit
Ready changes
Summary
Merged new upstream version: 1.2.9+git20221006.1.769cfa2 (was: 1.2.9).
Resulting package
Built on 2022-12-18T16:50 (took 7m59s)
The resulting binary packages can be installed (if you have the apt repository enabled) by running one of:
apt install -t fresh-snapshots megahit-dbgsymapt install -t fresh-snapshots megahit
Lintian Result
Diff
diff --git a/.gitignore b/.gitignore
deleted file mode 100644
index deae738..0000000
--- a/.gitignore
+++ /dev/null
@@ -1,40 +0,0 @@
-# Compiled Object files
-*.slo
-*.lo
-*.o
-*.obj
-
-# Compiled Dynamic libraries
-*.so
-*.dylib
-*.dll
-
-# Compiled Static libraries
-*.lai
-*.la
-*.a
-*.lib
-
-# Executables
-*.exe
-*.out
-*.app
-
-# ctags
-*.tags
-*.tags_sorted_by_file
-
-# Other library
-
-# Sublime Text file
-cmake-build-debug
-.idea
-
-build
-debug
-release
-venv
-clang
-sanitizer
-cov
-tsan
diff --git a/Dockerfile b/Dockerfile
index 823c6ed..a98a0eb 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,13 +1,27 @@
FROM ubuntu:18.04
-RUN apt-get update
-RUN apt-get install -y g++ make zlib1g-dev gzip bzip2 cmake python --no-install-recommends
+
COPY . /root/megahit
WORKDIR /root/megahit
-RUN rm -rf build
-RUN mkdir -p build
-WORKDIR build
-RUN cmake -DCMAKE_BUILD_TYPE=Release ..
-RUN make -j4
-RUN make install
-RUN megahit --test
-RUN megahit --test --kmin-1pass
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+ bzip2 \
+ cmake \
+ gzip \
+ g++ \
+ libgomp1 \
+ make \
+ python \
+ zlib1g-dev && \
+ rm -rf build && \
+ mkdir -p build && \
+ cd build && \
+ cmake -DCMAKE_BUILD_TYPE=Release .. && \
+ make -j4 install && \
+ apt-get autoremove --purge -y \
+ cmake \
+ g++ \
+ make \
+ zlib1g-dev
+
+RUN megahit --test && megahit --test --kmin-1pass
+ENTRYPOINT ["megahit"]
diff --git a/README.md b/README.md
index aa812ea..dfc3a0f 100644
--- a/README.md
+++ b/README.md
@@ -16,6 +16,11 @@ Installation
conda install -c bioconda megahit
```
+### Guix
+```sh
+guix install megahit
+```
+
### Pre-built binaries for x86_64 Linux
```sh
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 26564ee..5c5c910 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -1,3 +1,10 @@
+trigger:
+ paths:
+ exclude:
+ - '*.md'
+ - Dockerfile
+ - .travis.yml
+
jobs:
- job: ubuntu_1604
pool:
diff --git a/debian/changelog b/debian/changelog
index a79c2dc..c047fde 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+megahit (1.2.9+git20221006.1.769cfa2-1) UNRELEASED; urgency=low
+
+ * New upstream snapshot.
+
+ -- Debian Janitor <janitor@jelmer.uk> Sun, 18 Dec 2022 16:44:02 -0000
+
megahit (1.2.9-4) unstable; urgency=medium
* Disable reprotest
diff --git a/debian/patches/2to3.patch b/debian/patches/2to3.patch
index 1501226..101cb27 100644
--- a/debian/patches/2to3.patch
+++ b/debian/patches/2to3.patch
@@ -3,10 +3,10 @@ Author: Shayan Doust <hello@shayandoust.me>
Last-Update: 2019-10-11
---
-Index: megahit-1.2.9/src/megahit
+Index: megahit.git/src/megahit
===================================================================
---- megahit-1.2.9.orig/src/megahit 2019-10-22 13:15:58.504338175 +0100
-+++ megahit-1.2.9/src/megahit 2019-10-22 13:15:58.500338190 +0100
+--- megahit.git.orig/src/megahit
++++ megahit.git/src/megahit
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/python3
@@ -22,7 +22,7 @@ Index: megahit-1.2.9/src/megahit
import getopt
import json
-@@ -375,7 +375,7 @@
+@@ -375,7 +375,7 @@ def parse_option(argv):
elif option == '--max-tip-len':
opt.max_tip_len = int(value)
elif option == '--merge-level':
diff --git a/debian/patches/fix_test_path.patch b/debian/patches/fix_test_path.patch
index 0dce291..c7747a6 100644
--- a/debian/patches/fix_test_path.patch
+++ b/debian/patches/fix_test_path.patch
@@ -4,11 +4,11 @@ Author: Shayan Doust <hello@shayandoust.me>
Last-Update: 2019-10-15
---
-Index: megahit-1.2.9/src/megahit
+Index: megahit.git/src/megahit
===================================================================
---- megahit-1.2.9.orig/src/megahit 2019-10-22 13:15:53.688356856 +0100
-+++ megahit-1.2.9/src/megahit 2019-10-22 13:15:53.680356887 +0100
-@@ -570,14 +570,9 @@
+--- megahit.git.orig/src/megahit
++++ megahit.git/src/megahit
+@@ -570,14 +570,9 @@ def check_and_correct_option():
def find_test_data_path():
diff --git a/src/megahit b/src/megahit
index eb56a29..8ad261b 100755
--- a/src/megahit
+++ b/src/megahit
@@ -58,7 +58,7 @@ Optional Arguments:
Another way to set --k-list (overrides --k-list if one of them set):
--k-min <int> minimum kmer size (<= {0}), must be odd number [21]
--k-max <int> maximum kmer size (<= {0}), must be odd number [141]
- --k-step <int> increment of kmer size of each iteration (<= 28), must be even number [12]
+ --k-step <int> increment of kmer size of each iteration (<= 28), must be even number [10]
Advanced assembly options:
--no-mercy do not add mercy kmers
Debdiff
[The following lists of changes regard files as different if they have different names, permissions or owners.]
Files in second set of .debs but not in first
-rw-r--r-- root/root /usr/lib/debug/.build-id/0e/fe8a2e62d933d12b0e79b579a9ca6df2320037.debug -rw-r--r-- root/root /usr/lib/debug/.build-id/42/ae38fc3be9a13e8f442a797fb7fab6747077c0.debug -rw-r--r-- root/root /usr/lib/debug/.build-id/4e/bfb888afd2a6f093fb49ce66610f79f4d684fb.debug
Files in first set of .debs but not in second
-rw-r--r-- root/root /usr/lib/debug/.build-id/9e/943bfe45de55f2999dc727e42fbf6108c9ecab.debug -rw-r--r-- root/root /usr/lib/debug/.build-id/b0/4265b815ef5e75cf565874d486f58b798042f8.debug -rw-r--r-- root/root /usr/lib/debug/.build-id/df/0e3354664ad70d16cf8164e87783851a90ca4f.debug
Control files of package megahit: lines which differ (wdiff format)
Depends: bzip2, python3-all, python3:any, libc6 (>= 2.34), libgcc-s1 (>= 3.4), libgomp1 (>= 6), libstdc++6 (>= 11), 12.2.0-10), zlib1g (>= 1:1.1.4)
Control files of package megahit-dbgsym: lines which differ (wdiff format)
Build-Ids: 9e943bfe45de55f2999dc727e42fbf6108c9ecab b04265b815ef5e75cf565874d486f58b798042f8 df0e3354664ad70d16cf8164e87783851a90ca4f 0efe8a2e62d933d12b0e79b579a9ca6df2320037 42ae38fc3be9a13e8f442a797fb7fab6747077c0 4ebfb888afd2a6f093fb49ce66610f79f4d684fb