gentoo-overlay/sci-biology/embassy-hmmer/files/embassy-hmmer-2.3.2.660-slotted-hmmer2.patch

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 ");