Removed hard-coded directories/files. Now they can set in the configuration file. Added dataflow from phyml->phyml_cdna, and phyml_cdna->rap.
Removed hard-coded directories/files. Now they can set in the configuration file. Added dataflow from phyml->phyml_cdna, and phyml_cdna->rap.

danstaines/ensembl-compara,danstaines/ensembl-compara,kumarsaurabh20/ensembl-compara,Ensembl/ensembl-compara,Ensembl/ensembl-compara,etapanari/ensembl-compara,kumarsaurabh20/ensembl-compara,ckongEbi/ensembl-compara,Ensembl/ensembl-compara,kumarsaurabh20/ensembl-compara,dbolser-ebi/ensembl-compara,etapanari/ensembl-compara,ckongEbi/ensembl-compara,danstaines/ensembl-compara,Ensembl/ensembl-compara,kumarsaurabh20/ensembl-compara,etapanari/ensembl-compara,etapanari/ensembl-compara,danstaines/ensembl-compara,ckongEbi/ensembl-compara,Ensembl/ensembl-compara,Ensembl/ensembl-compara,dbolser-ebi/ensembl-compara,Ensembl/ensembl-compara,dbolser-ebi/ensembl-compara,danstaines/ensembl-compara,Ensembl/ensembl-compara