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 ");