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author | 2017-02-19 19:41:34 +0100 | |
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committer | 2017-02-19 19:42:46 +0100 | |
commit | 03ac4054f333f1d111ff7d9625d85ddeb6d5c42b (patch) | |
tree | e27070999dcad137338c14dfda49fda60d427997 /sci-biology/embassy-hmmer/files | |
parent | sci-biology/embassy-esim4: Port to emboss-r2.eclass (diff) | |
download | gentoo-03ac4054f333f1d111ff7d9625d85ddeb6d5c42b.tar.gz gentoo-03ac4054f333f1d111ff7d9625d85ddeb6d5c42b.tar.bz2 gentoo-03ac4054f333f1d111ff7d9625d85ddeb6d5c42b.zip |
sci-biology/embassy-hmmer: Port to emboss-r2.eclass
Package-Manager: portage-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/3937
Diffstat (limited to 'sci-biology/embassy-hmmer/files')
-rw-r--r-- | sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.660-slotted-hmmer2.patch | 101 |
1 files changed, 101 insertions, 0 deletions
diff --git a/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.660-slotted-hmmer2.patch b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.660-slotted-hmmer2.patch new file mode 100644 index 000000000000..f202ddf3d0b5 --- /dev/null +++ b/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.660-slotted-hmmer2.patch @@ -0,0 +1,101 @@ +Amend command-line names for Gentoo SLOTed hmmer:2 + +--- a/src/ehmmalign.c ++++ b/src/ehmmalign.c +@@ -99,7 +99,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmalign")); ++ ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmalign2")); + if(mapali) + ajFmtPrintAppS(&cmd, " --mapali %s ", ajFileGetNameC(mapali)); + if(withali) +--- a/src/ehmmbuild.c ++++ b/src/ehmmbuild.c +@@ -146,7 +146,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmbuild")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmbuild2")); + if(prior) + ajFmtPrintAppS(&cmd, " --prior %s ", ajFileGetNameC(prior)); + if(null) +--- a/src/ehmmcalibrate.c ++++ b/src/ehmmcalibrate.c +@@ -98,7 +98,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmcalibrate")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmcalibrate2")); + if(cpu) + ajFmtPrintAppS(&cmd, " --cpu %d ", cpu); + if(fixed) +--- a/src/ehmmconvert.c ++++ b/src/ehmmconvert.c +@@ -72,7 +72,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmconvert")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmconvert2")); + + /* ACD option only allows one selection */ + option = ajStrGetCharFirst(format); +--- a/src/ehmmemit.c ++++ b/src/ehmmemit.c +@@ -79,7 +79,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmemit")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmemit2")); + ajFmtPrintAppS(&cmd, " --seed %d ", seed); + if(a) + ajStrAppendC(&cmd, " -a "); +--- a/src/ehmmfetch.c ++++ b/src/ehmmfetch.c +@@ -74,7 +74,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmfetch")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmfetch2")); + if(nhmm) + ajStrAppendC(&cmd, " -n "); + /* Note the output redirected to outfname */ +--- a/src/ehmmindex.c ++++ b/src/ehmmindex.c +@@ -68,7 +68,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmindex")); ++ ajFmtPrintS(&cmd, "%S ", ajAcdGetpathC("hmmindex2")); + ajStrAppendC(&cmd, ajFileGetNameC(database)); + + +--- a/src/ehmmpfam.c ++++ b/src/ehmmpfam.c +@@ -122,7 +122,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmpfam")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmpfam2")); + if(nuc) + ajStrAppendC(&cmd, " -n "); + ajFmtPrintAppS(&cmd, " -A %d -E %f -T %f -Z %d", A, E, T, Z); +--- a/src/ehmmsearch.c ++++ b/src/ehmmsearch.c +@@ -102,7 +102,7 @@ + iii.HMMER 'options' (that don't appear in ACD file) + iv. HMMER & new parameters. + */ +- ajStrAssignS(&cmd, ajAcdGetpathC("hmmsearch")); ++ ajStrAssignS(&cmd, ajAcdGetpathC("hmmsearch2")); + ajFmtPrintAppS(&cmd, " -A %d -E %f -T %f -Z %d", A, E, T, Z); + if(compat) + ajStrAppendC(&cmd, " --compat "); |