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| author |   Donnie Berkholz <dberkholz@gentoo.org> | 2008-04-14 20:22:41 -0700 |
|---|---|---|
| committer | Donnie Berkholz <dberkholz@gentoo.org> | 2008-04-14 20:22:41 -0700 |
| commit | fed2cc459262c9bd3fe9db7c5691e4775ba8540b (patch) | |
| tree | 13c14a6eb823a8649a204ef73f9d9ab5b58ac83c /sci-biology | |
| parent | Add foldx-bin, required for biskit. (diff) | |
| download | dberkholz-fed2cc459262c9bd3fe9db7c5691e4775ba8540b.tar.gz dberkholz-fed2cc459262c9bd3fe9db7c5691e4775ba8540b.tar.bz2 dberkholz-fed2cc459262c9bd3fe9db7c5691e4775ba8540b.zip | |
probalign: use TMPDIR variable for temporary files.
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/probalign/Manifest | 3 | ||||
| -rw-r--r-- | sci-biology/probalign/files/use-tmpdir.patch | 48 | ||||
| -rw-r--r-- | sci-biology/probalign/probalign-1.3_beta.ebuild | 2 |
3 files changed, 52 insertions, 1 deletions
diff --git a/sci-biology/probalign/Manifest b/sci-biology/probalign/Manifest index 2e706bd..4b7ff3a 100644 --- a/sci-biology/probalign/Manifest +++ b/sci-biology/probalign/Manifest @@ -1,4 +1,5 @@ AUX 1.3-look-in-usr-bin-for-probalign.patch 584 RMD160 16b0112df505052f003e94e1ae9b691c3b98ff00 SHA1 fbcb633fa5c57c61d6d9a1c7e8df2f8c0b6a60e1 SHA256 312e2f0ae50ae66e3c384c2d3e73d5d360c2366a8659d35b0e5d19674fb0a47f AUX gcc-4.3.patch 438 RMD160 7cf8e4661e2f973ba95e450a20f21807c4838b8f SHA1 cfa326205d497ae7156627e67a0a097ae08acbc3 SHA256 fd382a6cc25050b4fae74a6e3047cba5a31e73c623f31898b0fcbdefedaebad5 +AUX use-tmpdir.patch 2169 RMD160 cf5d03111e432d3e8fc33fa13983ca8a184a6c3f SHA1 13cd71a105d3df6411206a175e52728e6e29f410 SHA256 1739b17842c7e3decb899616d1ea779156ddf7833ba0f93c516de40e2a727e13 DIST probaligngui_beta_1.3.tar.gz 1794865 RMD160 bb20fe4fd50015b839df78c4f179c21e6d0e041f SHA1 3456aa2d17c2ad42323e49f7530476679708210d SHA256 7343024dc7c2ae5fa415697bc1e1fe8accf93e515f093dea09ed1fc256c4f2a0 -EBUILD probalign-1.3_beta.ebuild 1498 RMD160 fd9648f5281483eafad87509684dde62a93d2b0a SHA1 84a377d4350924a2d4ad02768248488d6a89c923 SHA256 3c6f5df893f0744bcad2da59f7772cf6326fcc5d8bbc9aa02aae5b12cc3ce986 +EBUILD probalign-1.3_beta.ebuild 1608 RMD160 6063cf982c3fb5ed2c08065f7d76a093c25b6404 SHA1 0f8ffed7ea70426e5a11ed7a0356c0a28b113444 SHA256 5cb325388e6df995786a73d586fc13e9cab0953779d059d30481be55ad251789 diff --git a/sci-biology/probalign/files/use-tmpdir.patch b/sci-biology/probalign/files/use-tmpdir.patch new file mode 100644 index 0000000..392140b --- /dev/null +++ b/sci-biology/probalign/files/use-tmpdir.patch @@ -0,0 +1,48 @@ +diff -ur probaligngui_beta_1.3.orig/javagui/src/Frame1.java probaligngui_beta_1.3/javagui/src/Frame1.java +--- probaligngui_beta_1.3.orig/javagui/src/Frame1.java 2008-04-09 14:53:57.000000000 -0700 ++++ probaligngui_beta_1.3/javagui/src/Frame1.java 2008-04-09 14:56:47.000000000 -0700 +@@ -1078,7 +1078,7 @@ + InputStreamReader errisr = new InputStreamReader(stderr); + BufferedReader errbr = new BufferedReader(errisr); + +- PrintWriter out = new PrintWriter(new FileWriter(basedir+"/javagui/tempfiles/align.fasta")); ++ PrintWriter out = new PrintWriter(new FileWriter(System.getenv("TMPDIR")+"/align.fasta")); + + char extra = '|'; + String line = null; +@@ -2028,7 +2028,7 @@ + g2device.dispose(); + + ImageIO.write(image, "png", +- new File(basedir+"/javagui/tempfiles/tableImage.png"));// + number + ".png")); ++ new File(System.getenv("TMPDIR")+"/tableImage.png"));// + number + ".png")); + } + catch (Exception e) { + System.out.println(e); +@@ -2041,7 +2041,7 @@ + PrintWriter out = new PrintWriter(new FileWriter(savefile)); + + BufferedReader in = new BufferedReader(new FileReader( +- basedir+"/javagui/tempfiles/align.fasta")); ++ System.getenv("TMPDIR")+"/align.fasta")); + + while ( (line = in.readLine()) != null) { + +@@ -2218,7 +2218,7 @@ + header += horizontal_index + "\n\n"; + + com.lowagie.text.Image screenshot1 = com.lowagie.text.Image. +- getInstance(basedir+"/javagui/tempfiles/tableImage.png");// + imagenumber + ".png"); ++ getInstance(System.getenv("TMPDIR")+"/tableImage.png");// + imagenumber + ".png"); + imagenumber++; + + pdfdoc.add(new Chunk(header)); +@@ -2398,7 +2398,7 @@ + header += horizontal_index + "\n\n"; + + com.lowagie.text.Image screenshot1 = com.lowagie.text.Image. +- getInstance(basedir+"/javagui/tempfiles/tableImage.png");// + imagenumber + ".png"); ++ getInstance(System.getenv("TMPDIR")+"/tableImage.png");// + imagenumber + ".png"); + imagenumber++; + + pdfdoc.add(new Chunk(header)); diff --git a/sci-biology/probalign/probalign-1.3_beta.ebuild b/sci-biology/probalign/probalign-1.3_beta.ebuild index 449bc15..aa240e7 100644 --- a/sci-biology/probalign/probalign-1.3_beta.ebuild +++ b/sci-biology/probalign/probalign-1.3_beta.ebuild @@ -28,6 +28,8 @@ src_unpack() { cd "${S}" epatch "${FILESDIR}"/1.3-look-in-usr-bin-for-probalign.patch epatch "${FILESDIR}"/gcc-4.3.patch + # This doesn't use randomized locations in TMPDIR, so it is insecure. + epatch "${FILESDIR}"/use-tmpdir.patch } src_compile() { |