diff options
Diffstat (limited to 'var')
36 files changed, 98 insertions, 68 deletions
diff --git a/var/spack/repos/builtin.mock/packages/mirror-sourceforge-broken/package.py b/var/spack/repos/builtin.mock/packages/mirror-sourceforge-broken/package.py new file mode 100644 index 0000000000..be5d6aac16 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/mirror-sourceforge-broken/package.py @@ -0,0 +1,15 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class MirrorSourceforgeBroken(AutotoolsPackage, SourceforgePackage): + """Simple sourceforge.net package""" + + homepage = "http://www.tcl.tk" + url = "http://prdownloads.sourceforge.net/tcl/tcl8.6.5-src.tar.gz" + + version('8.6.8', sha256='c43cb0c1518ce42b00e7c8f6eaddd5195c53a98f94adc717234a65cbcfd3f96a') diff --git a/var/spack/repos/builtin.mock/packages/mirror-sourceforge/package.py b/var/spack/repos/builtin.mock/packages/mirror-sourceforge/package.py new file mode 100644 index 0000000000..6740292576 --- /dev/null +++ b/var/spack/repos/builtin.mock/packages/mirror-sourceforge/package.py @@ -0,0 +1,15 @@ +# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other +# Spack Project Developers. See the top-level COPYRIGHT file for details. +# +# SPDX-License-Identifier: (Apache-2.0 OR MIT) + +from spack import * + + +class MirrorSourceforge(AutotoolsPackage, SourceforgePackage): + """Simple sourceforge.net package""" + + homepage = "http://www.tcl.tk" + sourceforge_mirror_path = "tcl/tcl8.6.5-src.tar.gz" + + version('8.6.8', sha256='c43cb0c1518ce42b00e7c8f6eaddd5195c53a98f94adc717234a65cbcfd3f96a') diff --git a/var/spack/repos/builtin/packages/bbmap/package.py b/var/spack/repos/builtin/packages/bbmap/package.py index a9f51c614f..f4019c8391 100644 --- a/var/spack/repos/builtin/packages/bbmap/package.py +++ b/var/spack/repos/builtin/packages/bbmap/package.py @@ -6,11 +6,11 @@ from spack import * -class Bbmap(Package): +class Bbmap(Package, SourceforgePackage): """Short read aligner for DNA and RNA-seq data.""" homepage = "http://sourceforge.net/projects/bbmap/" - url = "https://downloads.sourceforge.net/project/bbmap/BBMap_38.63.tar.gz" + sourceforge_mirror_path = "bbmap/BBMap_38.63.tar.gz" version('38.63', sha256='089064104526c8d696164aefa067f935b888bc71ef95527c72a98c17ee90a01f') version('37.36', sha256='befe76d7d6f3d0f0cd79b8a01004a2283bdc0b5ab21b0743e9dbde7c7d79e8a9') diff --git a/var/spack/repos/builtin/packages/bridger/package.py b/var/spack/repos/builtin/packages/bridger/package.py index 04e44faf87..dbd4bb3f75 100644 --- a/var/spack/repos/builtin/packages/bridger/package.py +++ b/var/spack/repos/builtin/packages/bridger/package.py @@ -7,12 +7,12 @@ from spack import * from os import symlink -class Bridger(MakefilePackage): +class Bridger(MakefilePackage, SourceforgePackage): """Bridger : An Efficient De novo Transcriptome Assembler For RNA-Seq Data""" homepage = "https://sourceforge.net/projects/rnaseqassembly/" - url = "https://downloads.sourceforge.net/project/rnaseqassembly/Bridger_r2014-12-01.tar.gz" + sourceforge_mirror_path = "rnaseqassembly/Bridger_r2014-12-01.tar.gz" version('2014-12-01', sha256='8fbec8603ea8ad2162cbd0c658e4e0a4af6453bdb53310b4b7e0d112e40b5737') diff --git a/var/spack/repos/builtin/packages/freeglut/package.py b/var/spack/repos/builtin/packages/freeglut/package.py index 72ab7986d1..2d890534f4 100644 --- a/var/spack/repos/builtin/packages/freeglut/package.py +++ b/var/spack/repos/builtin/packages/freeglut/package.py @@ -6,12 +6,12 @@ from spack import * -class Freeglut(CMakePackage): +class Freeglut(CMakePackage, SourceforgePackage): """FreeGLUT is a free-software/open-source alternative to the OpenGL Utility Toolkit (GLUT) library""" homepage = "http://freeglut.sourceforge.net/" - url = "http://prdownloads.sourceforge.net/freeglut/freeglut-3.0.0.tar.gz" + sourceforge_mirror_path = "freeglut/freeglut-3.0.0.tar.gz" version('3.0.0', sha256='2a43be8515b01ea82bcfa17d29ae0d40bd128342f0930cd1f375f1ff999f76a2') diff --git a/var/spack/repos/builtin/packages/giflib/package.py b/var/spack/repos/builtin/packages/giflib/package.py index 71a0cb7965..69a1b0dc8d 100644 --- a/var/spack/repos/builtin/packages/giflib/package.py +++ b/var/spack/repos/builtin/packages/giflib/package.py @@ -6,12 +6,12 @@ from spack import * -class Giflib(AutotoolsPackage): +class Giflib(AutotoolsPackage, SourceforgePackage): """The GIFLIB project maintains the giflib service library, which has been pulling images out of GIFs since 1989.""" homepage = "http://giflib.sourceforge.net/" - url = "https://downloads.sourceforge.net/project/giflib/giflib-5.1.4.tar.bz2" + sourceforge_mirror_path = "giflib/giflib-5.1.4.tar.bz2" version('5.1.4', sha256='df27ec3ff24671f80b29e6ab1c4971059c14ac3db95406884fc26574631ba8d5') diff --git a/var/spack/repos/builtin/packages/imlib2/package.py b/var/spack/repos/builtin/packages/imlib2/package.py index 8cb3dc59b0..b039c0676f 100644 --- a/var/spack/repos/builtin/packages/imlib2/package.py +++ b/var/spack/repos/builtin/packages/imlib2/package.py @@ -5,14 +5,14 @@ from spack import * -class Imlib2(AutotoolsPackage): +class Imlib2(AutotoolsPackage, SourceforgePackage): """ Library that does image file loading and saving as well as rendering, manipulation, arbitrary polygon support """ homepage = "http://sourceforge.net/projects/enlightenment/" - url = "http://downloads.sourceforge.net/enlightenment/imlib2-1.5.1.tar.bz2" + sourceforge_mirror_path = "enlightenment/imlib2-1.5.1.tar.bz2" maintainers = ['TheQueasle'] diff --git a/var/spack/repos/builtin/packages/iperf2/package.py b/var/spack/repos/builtin/packages/iperf2/package.py index 6382010960..6c3369a93a 100644 --- a/var/spack/repos/builtin/packages/iperf2/package.py +++ b/var/spack/repos/builtin/packages/iperf2/package.py @@ -6,12 +6,12 @@ from spack import * -class Iperf2(AutotoolsPackage): +class Iperf2(AutotoolsPackage, SourceforgePackage): """This code is a continuation based from the no longer maintained iperf 2.0.5 code base. Iperf 2.0.5 is still widely deployed and used by many for testing networks and for qualifying networking products.""" homepage = "https://sourceforge.net/projects/iperf2" - url = "https://downloads.sourceforge.net/project/iperf2/iperf-2.0.12.tar.gz" + sourceforge_mirror_path = "iperf2/iperf-2.0.12.tar.gz" version('2.0.12', sha256='367f651fb1264b13f6518e41b8a7e08ce3e41b2a1c80e99ff0347561eed32646') diff --git a/var/spack/repos/builtin/packages/kaks-calculator/package.py b/var/spack/repos/builtin/packages/kaks-calculator/package.py index f551728a22..58edd8e249 100644 --- a/var/spack/repos/builtin/packages/kaks-calculator/package.py +++ b/var/spack/repos/builtin/packages/kaks-calculator/package.py @@ -6,14 +6,14 @@ from spack import * -class KaksCalculator(MakefilePackage): +class KaksCalculator(MakefilePackage, SourceforgePackage): """KaKs_Calculator adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates, attempting to include as many features as needed for accurately capturing evolutionary information in protein-coding sequences.""" homepage = "https://sourceforge.net/projects/kakscalculator2" - url = "https://downloads.sourceforge.net/project/kakscalculator2/KaKs_Calculator2.0.tar.gz" + sourceforge_mirror_path = "kakscalculator2/KaKs_Calculator2.0.tar.gz" version('2.0', sha256='e2df719a2fecc549d8ddc4e6d8f5cfa4b248282dca319c1928eaf886d68ec3c5') diff --git a/var/spack/repos/builtin/packages/libcerf/package.py b/var/spack/repos/builtin/packages/libcerf/package.py index d9209bf57b..e37e7f6339 100644 --- a/var/spack/repos/builtin/packages/libcerf/package.py +++ b/var/spack/repos/builtin/packages/libcerf/package.py @@ -7,14 +7,14 @@ from spack import * -class Libcerf(AutotoolsPackage): +class Libcerf(AutotoolsPackage, SourceforgePackage): """A self-contained C library providing complex error functions, based on Faddeeva's plasma dispersion function w(z). Also provides Dawson's integral and Voigt's convolution of a Gaussian and a Lorentzian """ homepage = "http://sourceforge.net/projects/libcerf" - url = "http://downloads.sourceforge.net/project/libcerf/libcerf-1.3.tgz" + sourceforge_mirror_path = "libcerf/libcerf-1.3.tgz" version('1.3', sha256='d7059e923d3f370c89fb4d19ed4f827d381bc3f0e36da5595a04aeaaf3e6a859') diff --git a/var/spack/repos/builtin/packages/libexif/package.py b/var/spack/repos/builtin/packages/libexif/package.py index fe9110f62d..5156ee4196 100644 --- a/var/spack/repos/builtin/packages/libexif/package.py +++ b/var/spack/repos/builtin/packages/libexif/package.py @@ -5,11 +5,11 @@ from spack import * -class Libexif(AutotoolsPackage): +class Libexif(AutotoolsPackage, SourceforgePackage): """A library to parse an EXIF file and read the data from those tags""" homepage = "https://sourceforge.net/projects/libexif" - url = "https://downloads.sourceforge.net/sourceforge/libexif/libexif-0.6.21.tar.bz2" + sourceforge_mirror_path = "libexif/libexif-0.6.21.tar.bz2" maintainers = ['TheQueasle'] diff --git a/var/spack/repos/builtin/packages/libuuid/package.py b/var/spack/repos/builtin/packages/libuuid/package.py index 3ec15ceb6b..fc4ca59efa 100644 --- a/var/spack/repos/builtin/packages/libuuid/package.py +++ b/var/spack/repos/builtin/packages/libuuid/package.py @@ -6,10 +6,10 @@ from spack import * -class Libuuid(AutotoolsPackage): +class Libuuid(AutotoolsPackage, SourceforgePackage): """Portable uuid C library""" homepage = "http://sourceforge.net/projects/libuuid/" - url = "http://downloads.sourceforge.net/project/libuuid/libuuid-1.0.3.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Flibuuid%2F&ts=1433881396&use_mirror=iweb" + sourceforge_mirror_path = "libuuid/libuuid-1.0.3.tar.gz" version('1.0.3', sha256='46af3275291091009ad7f1b899de3d0cea0252737550e7919d17237997db5644') diff --git a/var/spack/repos/builtin/packages/meraculous/package.py b/var/spack/repos/builtin/packages/meraculous/package.py index 46a1de77ea..df4e7109b5 100644 --- a/var/spack/repos/builtin/packages/meraculous/package.py +++ b/var/spack/repos/builtin/packages/meraculous/package.py @@ -6,12 +6,12 @@ from spack import * -class Meraculous(CMakePackage): +class Meraculous(CMakePackage, SourceforgePackage): """Meraculous is a while genome assembler for Next Generation Sequencing data geared for large genomes.""" homepage = "http://jgi.doe.gov/data-and-tools/meraculous/" - url = "https://downloads.sourceforge.net/project/meraculous20/Meraculous-v2.2.4.tar.gz" + sourceforge_mirror_path = "meraculous20/Meraculous-v2.2.4.tar.gz" git = "https://bitbucket.org/berkeleylab/genomics-meraculous2.git" version('2.2.5.1', branch='release-2.2.5.1') diff --git a/var/spack/repos/builtin/packages/microbiomeutil/package.py b/var/spack/repos/builtin/packages/microbiomeutil/package.py index 2155e877d9..bcae7ad991 100644 --- a/var/spack/repos/builtin/packages/microbiomeutil/package.py +++ b/var/spack/repos/builtin/packages/microbiomeutil/package.py @@ -6,11 +6,11 @@ from spack import * -class Microbiomeutil(MakefilePackage): +class Microbiomeutil(MakefilePackage, SourceforgePackage): """Microbiome analysis utilities""" homepage = "http://microbiomeutil.sourceforge.net/" - url = "https://downloads.sourceforge.net/project/microbiomeutil/microbiomeutil-r20110519.tgz" + sourceforge_mirror_path = "microbiomeutil/microbiomeutil-r20110519.tgz" version('20110519', sha256='9233de80ea57bfb9e9371cbe7e3bfad2d4a51168fddaf60fa144c4046c80d823') diff --git a/var/spack/repos/builtin/packages/nccmp/package.py b/var/spack/repos/builtin/packages/nccmp/package.py index 0e2a13f6f0..db9603b42f 100644 --- a/var/spack/repos/builtin/packages/nccmp/package.py +++ b/var/spack/repos/builtin/packages/nccmp/package.py @@ -6,10 +6,10 @@ from spack import * -class Nccmp(Package): +class Nccmp(Package, SourceforgePackage): """Compare NetCDF Files""" homepage = "http://nccmp.sourceforge.net/" - url = "http://downloads.sourceforge.net/project/nccmp/nccmp-1.8.2.0.tar.gz" + sourceforge_mirror_path = "nccmp/nccmp-1.8.2.0.tar.gz" version('1.8.2.0', sha256='7f5dad4e8670568a71f79d2bcebb08d95b875506d3d5faefafe1a8b3afa14f18') diff --git a/var/spack/repos/builtin/packages/nicstat/package.py b/var/spack/repos/builtin/packages/nicstat/package.py index 37e931bb83..054cc9c4d8 100644 --- a/var/spack/repos/builtin/packages/nicstat/package.py +++ b/var/spack/repos/builtin/packages/nicstat/package.py @@ -6,7 +6,7 @@ from spack import * -class Nicstat(MakefilePackage): +class Nicstat(MakefilePackage, SourceforgePackage): """ Nicstat is a Solaris and Linux command-line that prints out network statistics for all network interface cards (NICs), including packets, @@ -14,7 +14,7 @@ class Nicstat(MakefilePackage): """ homepage = "https://github.com/scotte/nicstat" - url = "https://jaist.dl.sourceforge.net/project/nicstat/nicstat-1.95.tar.gz" + sourceforge_mirror_path = "nicstat/nicstat-1.95.tar.gz" version('1.95', sha256='c4cc33f8838f4523f27c3d7584eedbe59f4c587f0821612f5ac2201adc18b367') diff --git a/var/spack/repos/builtin/packages/octave-optim/package.py b/var/spack/repos/builtin/packages/octave-optim/package.py index 2a5b736ec7..4f94c18ac4 100644 --- a/var/spack/repos/builtin/packages/octave-optim/package.py +++ b/var/spack/repos/builtin/packages/octave-optim/package.py @@ -6,11 +6,11 @@ from spack import * -class OctaveOptim(OctavePackage): +class OctaveOptim(OctavePackage, SourceforgePackage): """Non-linear optimization toolkit for Octave.""" homepage = "https://octave.sourceforge.io/optim/" - url = "https://downloads.sourceforge.net/octave/optim-1.5.2.tar.gz" + sourceforge_mirror_path = "octave/optim-1.5.2.tar.gz" version('1.5.2', sha256='7b36033c5581559dc3e7616f97d402bc44dde0dfd74c0e3afdf47d452a76dddf') diff --git a/var/spack/repos/builtin/packages/octave-splines/package.py b/var/spack/repos/builtin/packages/octave-splines/package.py index e100e9b840..5a9a5777c1 100644 --- a/var/spack/repos/builtin/packages/octave-splines/package.py +++ b/var/spack/repos/builtin/packages/octave-splines/package.py @@ -6,11 +6,11 @@ from spack import * -class OctaveSplines(OctavePackage): +class OctaveSplines(OctavePackage, SourceforgePackage): """Additional spline functions.""" homepage = "http://octave.sourceforge.net/splines/index.html" - url = "http://downloads.sourceforge.net/octave/splines-1.3.1.tar.gz" + sourceforge_mirror_path = "octave/splines-1.3.1.tar.gz" version('1.3.1', sha256='f9665d780c37aa6a6e17d1f424c49bdeedb89d1192319a4e39c08784122d18f9') extends('octave@3.6.0:') diff --git a/var/spack/repos/builtin/packages/octave-struct/package.py b/var/spack/repos/builtin/packages/octave-struct/package.py index 2d99125be6..b428ce7872 100644 --- a/var/spack/repos/builtin/packages/octave-struct/package.py +++ b/var/spack/repos/builtin/packages/octave-struct/package.py @@ -6,11 +6,11 @@ from spack import * -class OctaveStruct(OctavePackage): +class OctaveStruct(OctavePackage, SourceforgePackage): """Additional structure manipulation functions for Octave.""" homepage = "https://octave.sourceforge.io/struct/" - url = "https://downloads.sourceforge.net/octave/struct-1.0.14.tar.gz" + sourceforge_mirror_path = "octave/struct-1.0.14.tar.gz" version('1.0.14', sha256='ad4e17687bc24650f032757271b20b70fe32c35513d4dd9ab1e549919df36b47') extends('octave@2.9.7:') diff --git a/var/spack/repos/builtin/packages/optipng/package.py b/var/spack/repos/builtin/packages/optipng/package.py index 364c2cb02d..a94379f174 100644 --- a/var/spack/repos/builtin/packages/optipng/package.py +++ b/var/spack/repos/builtin/packages/optipng/package.py @@ -6,7 +6,7 @@ from spack import * -class Optipng(AutotoolsPackage): +class Optipng(AutotoolsPackage, SourceforgePackage): """ OptiPNG is a PNG optimizer that recompresses image files to a smaller size, without losing any information. This program also converts external @@ -15,6 +15,6 @@ class Optipng(AutotoolsPackage): """ homepage = "http://optipng.sourceforge.net/" - url = "http://prdownloads.sourceforge.net/optipng/optipng-0.7.7.tar.gz" + sourceforge_mirror_path = "optipng/optipng-0.7.7.tar.gz" version('0.7.7', sha256='4f32f233cef870b3f95d3ad6428bfe4224ef34908f1b42b0badf858216654452') diff --git a/var/spack/repos/builtin/packages/pbsuite/package.py b/var/spack/repos/builtin/packages/pbsuite/package.py index ee45037755..fb81eb65dc 100644 --- a/var/spack/repos/builtin/packages/pbsuite/package.py +++ b/var/spack/repos/builtin/packages/pbsuite/package.py @@ -6,13 +6,13 @@ from spack import * -class Pbsuite(Package): +class Pbsuite(Package, SourceforgePackage): """PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles.""" homepage = "https://sourceforge.net/p/pb-jelly/wiki/Home/" - url = "https://downloads.sourceforge.net/project/pb-jelly/PBSuite_15.8.24.tgz" + sourceforge_mirror_path = "pb-jelly/PBSuite_15.8.24.tgz" version('15.8.24', sha256='1be082faa62cb3f701c78498db8544c844c3d6d3e3524fecf00a12e82a97e12b') diff --git a/var/spack/repos/builtin/packages/py-crossmap/package.py b/var/spack/repos/builtin/packages/py-crossmap/package.py index 13261f80c6..bae028a641 100644 --- a/var/spack/repos/builtin/packages/py-crossmap/package.py +++ b/var/spack/repos/builtin/packages/py-crossmap/package.py @@ -6,12 +6,12 @@ from spack import * -class PyCrossmap(PythonPackage): +class PyCrossmap(PythonPackage, SourceforgePackage): """CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies""" homepage = "http://crossmap.sourceforge.net/" - url = "https://downloads.sourceforge.net/project/crossmap/CrossMap-0.3.3.tar.gz" + sourceforge_mirror_path = "crossmap/CrossMap-0.3.3.tar.gz" version('0.3.3', sha256='56d99fd606e13e399b83438953d0d89fc281df1c1e8e47eed7d773e7ec9c88f8') version('0.2.9', sha256='57243ee5051352c93088874c797ceac0426f249704ba897360fb628b3365d0af') diff --git a/var/spack/repos/builtin/packages/qrupdate/package.py b/var/spack/repos/builtin/packages/qrupdate/package.py index 3f21501711..760500dfa4 100644 --- a/var/spack/repos/builtin/packages/qrupdate/package.py +++ b/var/spack/repos/builtin/packages/qrupdate/package.py @@ -8,12 +8,12 @@ import sys from spack import * -class Qrupdate(MakefilePackage): +class Qrupdate(MakefilePackage, SourceforgePackage): """qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.""" homepage = "http://sourceforge.net/projects/qrupdate/" - url = "https://downloads.sourceforge.net/qrupdate/qrupdate-1.1.2.tar.gz" + sourceforge_mirror_path = "qrupdate/qrupdate-1.1.2.tar.gz" version('1.1.2', sha256='e2a1c711dc8ebc418e21195833814cb2f84b878b90a2774365f0166402308e08') diff --git a/var/spack/repos/builtin/packages/ray/package.py b/var/spack/repos/builtin/packages/ray/package.py index f737ee8063..afa849e08d 100644 --- a/var/spack/repos/builtin/packages/ray/package.py +++ b/var/spack/repos/builtin/packages/ray/package.py @@ -6,11 +6,11 @@ from spack import * -class Ray(CMakePackage): +class Ray(CMakePackage, SourceforgePackage): """Parallel genome assemblies for parallel DNA sequencing""" homepage = "http://denovoassembler.sourceforge.net/" - url = "https://downloads.sourceforge.net/project/denovoassembler/Ray-2.3.1.tar.bz2" + sourceforge_mirror_path = "denovoassembler/Ray-2.3.1.tar.bz2" version('2.3.1', sha256='3122edcdf97272af3014f959eab9a0f0e5a02c8ffc897d842b06b06ccd748036') diff --git a/var/spack/repos/builtin/packages/rdp-classifier/package.py b/var/spack/repos/builtin/packages/rdp-classifier/package.py index 8c182d323a..2895010cd7 100644 --- a/var/spack/repos/builtin/packages/rdp-classifier/package.py +++ b/var/spack/repos/builtin/packages/rdp-classifier/package.py @@ -6,13 +6,13 @@ from spack import * -class RdpClassifier(Package): +class RdpClassifier(Package, SourceforgePackage): """The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. """ homepage = "http://rdp.cme.msu.edu/" - url = "https://downloads.sourceforge.net/project/rdp-classifier/rdp-classifier/rdp_classifier_2.12.zip" + sourceforge_mirror_path = "rdp-classifier/rdp_classifier_2.12.zip" version('2.12', sha256='977896248189a1ce2146dd3a61d203c3c6bc9aa3982c60332d463832922f7d0a') diff --git a/var/spack/repos/builtin/packages/saga-gis/package.py b/var/spack/repos/builtin/packages/saga-gis/package.py index 49d070daf5..50ce549a1e 100644 --- a/var/spack/repos/builtin/packages/saga-gis/package.py +++ b/var/spack/repos/builtin/packages/saga-gis/package.py @@ -5,7 +5,7 @@ from spack import * -class SagaGis(AutotoolsPackage): +class SagaGis(AutotoolsPackage, SourceforgePackage): """ SAGA is a GIS for Automated Geoscientific Analyses and has been designed for an easy and effective implementation of spatial algorithms. It offers @@ -13,7 +13,7 @@ class SagaGis(AutotoolsPackage): easily approachable user interface with many visualisation options """ homepage = "http://saga-gis.org/" - url = "https://sourceforge.net/projects/saga-gis/files/SAGA%20-%205/SAGA%20-%205.0.0/saga-5.0.0.tar.gz" + sourceforge_mirror_path = "SAGA%20-%205.0.0/saga-5.0.0.tar.gz" git = "git://git.code.sf.net/p/saga-gis/code" version('develop', branch='master') diff --git a/var/spack/repos/builtin/packages/scalpel/package.py b/var/spack/repos/builtin/packages/scalpel/package.py index 6ce6d23c8b..1634fe11f4 100644 --- a/var/spack/repos/builtin/packages/scalpel/package.py +++ b/var/spack/repos/builtin/packages/scalpel/package.py @@ -6,14 +6,14 @@ from spack import * -class Scalpel(MakefilePackage): +class Scalpel(MakefilePackage, SourceforgePackage): """Scalpel is a software package for detecting INDELs (INsertions and DELetions) mutations in a reference genome which has been sequenced with next-generation sequencing technology. """ homepage = "http://scalpel.sourceforge.net/index.html" - url = "https://downloads.sourceforge.net/project/scalpel/scalpel-0.5.4.tar.gz" + sourceforge_mirror_path = "scalpel/scalpel-0.5.4.tar.gz" version('0.5.4', sha256='506f731b3886def158c15fd8b74fa98390f304a507d2040972e6b09ddefac8f0') version('0.5.3', sha256='d45b569fe3aa5934883bc7216c243d53168351c23e020d96a46fa77a1563b65e') diff --git a/var/spack/repos/builtin/packages/smalt/package.py b/var/spack/repos/builtin/packages/smalt/package.py index 1e6e11f365..47d5c99329 100644 --- a/var/spack/repos/builtin/packages/smalt/package.py +++ b/var/spack/repos/builtin/packages/smalt/package.py @@ -6,10 +6,10 @@ from spack import * -class Smalt(AutotoolsPackage): +class Smalt(AutotoolsPackage, SourceforgePackage): """SMALT aligns DNA sequencing reads with a reference genome.""" homepage = "http://www.sanger.ac.uk/science/tools/smalt-0" - url = "https://downloads.sourceforge.net/project/smalt/smalt-0.7.6.tar.gz" + sourceforge_mirror_path = "smalt/smalt-0.7.6.tar.gz" version('0.7.6', sha256='89ccdfe471edba3577b43de9ebfdaedb5cd6e26b02bf4000c554253433796b31') diff --git a/var/spack/repos/builtin/packages/snpeff/package.py b/var/spack/repos/builtin/packages/snpeff/package.py index d2e4d1cede..b8f23c5b68 100644 --- a/var/spack/repos/builtin/packages/snpeff/package.py +++ b/var/spack/repos/builtin/packages/snpeff/package.py @@ -7,13 +7,13 @@ from spack import * import os.path -class Snpeff(Package): +class Snpeff(Package, SourceforgePackage): """SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).""" homepage = "http://snpeff.sourceforge.net/" - url = "https://downloads.sourceforge.net/project/snpeff/snpEff_latest_core.zip" + sourceforge_mirror_path = "snpeff/snpEff_latest_core.zip" version('2017-11-24', sha256='d55a7389a78312947c1e7dadf5e6897b42d3c6e942e7c1b8ec68bb35d2ae2244') diff --git a/var/spack/repos/builtin/packages/swig/package.py b/var/spack/repos/builtin/packages/swig/package.py index ebc04dd077..c6c9824a63 100644 --- a/var/spack/repos/builtin/packages/swig/package.py +++ b/var/spack/repos/builtin/packages/swig/package.py @@ -9,7 +9,7 @@ import os from spack import * -class Swig(AutotoolsPackage): +class Swig(AutotoolsPackage, SourceforgePackage): """SWIG is an interface compiler that connects programs written in C and C++ with scripting languages such as Perl, Python, Ruby, and Tcl. It works by taking the declarations found in C/C++ @@ -20,7 +20,7 @@ class Swig(AutotoolsPackage): application.""" homepage = "http://www.swig.org" - url = "http://prdownloads.sourceforge.net/swig/swig-3.0.12.tar.gz" + sourceforge_mirror_path = "swig/swig-3.0.12.tar.gz" version('master', git='https://github.com/swig/swig.git') version('4.0.1', sha256='7a00b4d0d53ad97a14316135e2d702091cd5f193bb58bcfcd8bc59d41e7887a9') diff --git a/var/spack/repos/builtin/packages/tcl/package.py b/var/spack/repos/builtin/packages/tcl/package.py index 28ee2bd2a4..ac3a98ebf6 100644 --- a/var/spack/repos/builtin/packages/tcl/package.py +++ b/var/spack/repos/builtin/packages/tcl/package.py @@ -9,7 +9,7 @@ from spack.util.environment import is_system_path from spack import * -class Tcl(AutotoolsPackage): +class Tcl(AutotoolsPackage, SourceforgePackage): """Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, @@ -18,7 +18,7 @@ class Tcl(AutotoolsPackage): that is truly cross platform, easily deployed and highly extensible.""" homepage = "http://www.tcl.tk" - url = "http://prdownloads.sourceforge.net/tcl/tcl8.6.5-src.tar.gz" + sourceforge_mirror_path = "tcl/tcl8.6.5-src.tar.gz" version('8.6.8', sha256='c43cb0c1518ce42b00e7c8f6eaddd5195c53a98f94adc717234a65cbcfd3f96a') version('8.6.6', sha256='a265409781e4b3edcc4ef822533071b34c3dc6790b893963809b9fe221befe07') diff --git a/var/spack/repos/builtin/packages/tclap/package.py b/var/spack/repos/builtin/packages/tclap/package.py index 6097dfbcde..f8d8ce800d 100644 --- a/var/spack/repos/builtin/packages/tclap/package.py +++ b/var/spack/repos/builtin/packages/tclap/package.py @@ -6,11 +6,11 @@ from spack import * -class Tclap(AutotoolsPackage): +class Tclap(AutotoolsPackage, SourceforgePackage): """Templatized C++ Command Line Parser""" homepage = "http://tclap.sourceforge.net" - url = "https://downloads.sourceforge.net/project/tclap/tclap-1.2.2.tar.gz" + sourceforge_mirror_path = "tclap/tclap-1.2.2.tar.gz" version('1.2.2', sha256='f5013be7fcaafc69ba0ce2d1710f693f61e9c336b6292ae4f57554f59fde5837') version('1.2.1', sha256='9f9f0fe3719e8a89d79b6ca30cf2d16620fba3db5b9610f9b51dd2cd033deebb') diff --git a/var/spack/repos/builtin/packages/tk/package.py b/var/spack/repos/builtin/packages/tk/package.py index 0e1cb3f2c4..665f25f59c 100644 --- a/var/spack/repos/builtin/packages/tk/package.py +++ b/var/spack/repos/builtin/packages/tk/package.py @@ -7,7 +7,7 @@ from spack import * import os -class Tk(AutotoolsPackage): +class Tk(AutotoolsPackage, SourceforgePackage): """Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches. Tk is the standard GUI not only for Tcl, but for @@ -15,7 +15,7 @@ class Tk(AutotoolsPackage): applications that run unchanged across Windows, Mac OS X, Linux and more.""" homepage = "http://www.tcl.tk" - url = "http://prdownloads.sourceforge.net/tcl/tk8.6.5-src.tar.gz" + sourceforge_mirror_path = "tcl/tk8.6.5-src.tar.gz" version('8.6.8', sha256='49e7bca08dde95195a27f594f7c850b088be357a7c7096e44e1158c7a5fd7b33') version('8.6.6', sha256='d62c371a71b4744ed830e3c21d27968c31dba74dd2c45f36b9b071e6d88eb19d') diff --git a/var/spack/repos/builtin/packages/wxpropgrid/package.py b/var/spack/repos/builtin/packages/wxpropgrid/package.py index 2055205d30..644af13221 100644 --- a/var/spack/repos/builtin/packages/wxpropgrid/package.py +++ b/var/spack/repos/builtin/packages/wxpropgrid/package.py @@ -6,13 +6,13 @@ from spack import * -class Wxpropgrid(Package): +class Wxpropgrid(Package, SourceforgePackage): """wxPropertyGrid is a property sheet control for wxWidgets. In other words, it is a specialized two-column grid for editing properties such as strings, numbers, flagsets, string arrays, and colours.""" homepage = "http://wxpropgrid.sourceforge.net/" - url = "http://prdownloads.sourceforge.net/wxpropgrid/wxpropgrid-1.4.15-src.tar.gz" + sourceforge_mirror_path = "wxpropgrid/wxpropgrid-1.4.15-src.tar.gz" version('1.4.15', sha256='f0c9a86656828f592c8e57d2c89401f07f0af6a45b17bbca3990e8d29121c2b8') diff --git a/var/spack/repos/builtin/packages/xqilla/package.py b/var/spack/repos/builtin/packages/xqilla/package.py index 2235a609e5..645edc19e5 100644 --- a/var/spack/repos/builtin/packages/xqilla/package.py +++ b/var/spack/repos/builtin/packages/xqilla/package.py @@ -6,12 +6,12 @@ from spack import * -class Xqilla(AutotoolsPackage): +class Xqilla(AutotoolsPackage, SourceforgePackage): """XQilla is an XQuery and XPath 2 library and command line utility written in C++, implemented on top of the Xerces-C library.""" homepage = "http://xqilla.sourceforge.net/HomePage" - url = "https://downloads.sourceforge.net/project/xqilla/XQilla-2.3.3.tar.gz" + sourceforge_mirror_path = "xqilla/XQilla-2.3.3.tar.gz" version('2.3.3', sha256='8f76b9b4f966f315acc2a8e104e426d8a76ba4ea3441b0ecfdd1e39195674fd6') diff --git a/var/spack/repos/builtin/packages/xz/package.py b/var/spack/repos/builtin/packages/xz/package.py index cbaaaa3ec6..3839469231 100644 --- a/var/spack/repos/builtin/packages/xz/package.py +++ b/var/spack/repos/builtin/packages/xz/package.py @@ -6,14 +6,14 @@ from spack import * -class Xz(AutotoolsPackage): +class Xz(AutotoolsPackage, SourceforgePackage): """XZ Utils is free general-purpose data compression software with high compression ratio. XZ Utils were written for POSIX-like systems, but also work on some not-so-POSIX systems. XZ Utils are the successor to LZMA Utils.""" homepage = "http://tukaani.org/xz/" - url = "http://tukaani.org/xz/xz-5.2.5.tar.bz2" + sourceforge_mirror_path = "lzmautils/files/xz-5.2.5.tar.bz2" list_url = "http://tukaani.org/xz/old.html" version('5.2.5', sha256='5117f930900b341493827d63aa910ff5e011e0b994197c3b71c08a20228a42df') |